Transcriptome response to copper heavy metal stress in hard-shelled mussel (Mytilus coruscus)

Comparative transcriptome analysis reveals differences in immune responses to copper ions in Sepia esculenta under high-temperature conditions

Sepia esculenta is one of the most abundant extant squid populations in Southeast Asia and is of interest due to its rapid reproductive rate and high commercial value. In recent years, with the rapid development of industrialization, issues such as global warming and heavy metal pollution in the oceans have emerged, posing a serious threat to the life activities of marine organisms. In this study, we used transcriptomic techniques to investigate the differences in Cu exposure immune responses in S. esculenta larvae under different temperature conditions. The enrichment of solute carrier family (SLC) genes and genes related to DNA replication and damage was significantly higher in the CuT group than in the Cu group. Functional enrichment analysis revealed that the FcγR-mediated phagocytosis and autophagy pathways were enriched in the CuT group. Based on the analysis of differentially expressed genes (DEGs) and functional enrichment results, we can preliminarily infer that the CuT group caused more severe disruption of intercellular ion transport and DNA replication and repair in larvae compared to the Cu group. This may have further interfered with the normal physiological activities of S. esculenta larvae. Overall, at high temperatures, Cu exposure induces a more intense inflammatory response. The results of this study provide a theoretical foundation for researchers to further understand the effects of environmental factors on the immunity of S. esculenta larvae, as well as preliminary insights into the enhanced toxic effects of metallic copper on aquatic organisms under high-temperature conditions.

Integrated transcriptomic and metabolomic approaches reveal molecular response and potential biomarkers of the deep-sea mussel Gigantidas platifrons to copper exposure

Metal pollution caused by deep-sea mining activities has potential detrimental effects on deep-sea ecosystems. However, our knowledge of how deep-sea organisms respond to this pollution is limited, given the challenges of remoteness and technology. To address this, we conducted a toxicity experiment by using deep-sea mussel Gigantidas platifrons as model animals and exposing them to different copper (Cu) concentrations (50 and 500 μg/L) for 7 days. Transcriptomics and LC-MS-based metabolomics methods were employed to characterize the profiles of transcription and metabolism in deep-sea mussels exposed to Cu. Transcriptomic results suggested that Cu toxicity significantly affected the immune response, apoptosis, and signaling processes in G. platifrons. Metabolomic results demonstrated that Cu exposure disrupted its carbohydrate metabolism, anaerobic metabolism and amino acid metabolism. By integrating both sets of results, transcriptomic and metabolomic, we find that Cu exposure significantly disrupts the metabolic pathway of protein digestion and absorption in G. platifrons. Furthermore, several key genes (e.g., heat shock protein 70 and baculoviral IAP repeat-containing protein 2/3) and metabolites (e.g., alanine and succinate) were identified as potential molecular biomarkers for deep-sea mussel's responses to Cu toxicity. This study contributes novel insight for assessing the potential effects of deep-sea mining activities on deep-sea organisms.

Expansion and diversity of caspases in Mytilus coruscus contribute to larval metamorphosis and environmental adaptation

BACKGROUND

Apoptosis is involved (directly and indirectly) in several physiological processes including tissue remodeling during the development, the turnover of immune cells, and a defense against harmful stimuli. The disordered apoptotic process participates in the pathogenesis of various diseases, such as neoplasms, and chronic inflammatory or systemic autoimmune diseases, which are associated with its inadequate regulation. Caspases are vital components of the apoptotic pathway that are involved in developmental and immune processes. However, genome-wide identification and functional analysis of caspase have not been conducted in Mytilus coruscus, which is an economically important bivalve.

RESULTS

Here, 47 caspase genes were identified from the genomes of M. coruscus, and the expansion of caspase-2/9 and caspase-3/6/7 genes were observed. Tandem duplication acts as an essential driver of gene expansion. The expanded caspase genes were highly diverse in terms of sequence, domain structure, and spatiotemporal expression profiles, suggesting their functional differentiation. The high expression of the expanded caspase genes at the pediveliger larvae stage and the result of apoptosis location in the velum suggest that the apoptosis mediated by them plays a critical role in the metamorphosis of M. coruscus larvae. In gill, caspase genes respond differently to the challenge of different strains, and most caspase-2/9 and caspase-3/6/7 genes were induced by copper stress, whereas caspase-8/10 genes were suppressed. Additionally, most caspase genes were upregulated in the mantle under ocean acidification which could weaken the biomineralization capacity of the mantle tissue.

CONCLUSIONS

These results provide a comprehensive overview of the evolution and function of the caspase family and enhanced the understanding of the biological function of caspases in M. coruscus larval development and response to biotic and abiotic challenges.

To live or die: "Fine-tuning" adaptation revealed by systemic analyses in symbiotic bathymodiolin mussels from diverse deep-sea extreme ecosystems

Hydrothermal vents (HVs) and cold seeps (CSs) are typical deep-sea extreme ecosystems with their own geochemical characteristics to supply the unique living conditions for local communities. Once HVs or CSs stop emission, the dramatic environmental change would pose survival risks to deep-sea organisms. Up to now, limited knowledge has been available to understand the biological responses and adaptive strategy to the extreme environments and their transition from active to extinct stage, mainly due to the technical difficulties and lack of representative organisms. In this study, bathymodiolin mussels, the dominant and successful species surviving in diverse deep-sea extreme ecosystems, were collected from active and extinct HVs (Southwest Indian Ocean) or CSs (South China Sea) via two individual cruises. The transcriptomic analysis and determination of multiple biological indexes in stress defense and metabolic systems were conducted in both gills and digestive glands of mussels, together with the metagenomic analysis of symbionts in mussels. The results revealed the ecosystem- and tissue-specific transcriptional regulation in mussels, addressing the autologous adaptations in antioxidant defense, energy utilization and key compounds (i.e. sulfur) metabolism. In detail, the successful antioxidant defense contributed to conquering the oxidative stress induced during the unavoidable metabolism of xenobiotics commonly existing in the extreme ecosystems; changes in metabolic rate functioned to handle toxic matters in different surroundings; upregulated gene expression of sulfide:quinone oxidoreductase indicated an active sulfide detoxification in mussels from HVs and active stage of HVs & CSs. Coordinately, a heterologous adaptation, characterized by the functional compensation between symbionts and mussels in energy utilization, sulfur and carbon metabolism, was also evidenced by the bacterial metagenomic analysis. Taken together, a new insight was proposed that symbiotic bathymodiolin mussels would develop a "finetuning" strategy combining the autologous and heterologous regulations to fulfill the efficient and effective adaptations for successful survival.

Sources, bioaccumulation, and toxicity mechanisms of cadmium in Chlamys farreri

The Potentially toxic elements (PTEs) cadmium (Cd) is one of the most serious stressors polluting the marine environment. Marine bivalves have specific high enrichment capacity for Cd. Previous studies have investigated the tissue distribution changes and toxic effects of Cd in bivalves, but the sources of Cd enrichment, migration regulation during growth, and toxicity mechanisms in bivalves have not been fully explained. Here, we used stable-isotope labeling to investigate the contributions of Cd from different sources to scallop tissues. We sampled the entire growth cycle of Chlamys farreri, which is widely cultured in northern China, from juveniles to adult scallops. We found tissue variability in the bioconcentration-metabolism pattern of Cd in different bound states, with Cd in the aqueous accounting for a significant contribution. The accumulation pattern of Cd in all tissues during growth was more significant in the viscera and gills. Additionally, we combined a multi-omics approach to reveal a network of oxidative stress-induced toxicity mechanisms of Cd in scallops, identifying differentially expressed genes and proteins involved in metal ion binding, oxidative stress, energy metabolism, and apoptosis. Our findings have important implications for both ecotoxicology and aquaculture. They also provide new insights into marine environmental assessment and mariculture development.

Oxidative Damage of Mussels Living in Seawater Enriched with Trace Metals, from the Viewpoint of Proteins Expression and Modification

The impact of metals bioaccumulation in marine organisms is a subject of intense investigation. This study was designed to determine the association between oxidative stress induced by seawater enriched with trace metals and protein synthesis using as a model the mussels Mytilus galloprovincialis. Mussels were exposed to 40 μg/L Cu, 30 μg/L Hg, or 100 μg/L Cd for 5 and 15 days, and the pollution effect was evaluated by measuring established oxidative biomarkers. The results showed damage on the protein synthesis machine integrity and specifically on translation factors and ribosomal proteins expression and modifications. The exposure of mussels to all metals caused oxidative damage that was milder in the cases of Cu and Hg and more pronounced for Cd. However, after prolonged exposure of mussels to Cd (15 days), the effects receded. These changes that perturb protein biosynthesis can serve as a great tool for elucidating the mechanisms of toxicity and could be integrated in biomonitoring programs.

Evaluation of interactive effects of phosphorus-32 and copper on marine and freshwater bivalve mollusks

PURPOSE

Contaminants seldom occur in isolation in the aquatic environment. While pollution of coastal and inland water bodies has received considerable attention to date, there is limited information on potential interactive effects between radionuclides and metals. Whether by accidental or controlled release, such contaminants co-exist in aquatic ecosystems and can pose an enhanced threat to biota. Using a range of biological responses, the study aimed to evaluate relative interactive effects on representative freshwater and marine bivalve species.

METHODS

An integrated, multi-biomarker approach was adopted to investigate response to copper (Cu, 18 μg L^-1), a known environmentally relevant genotoxic metal and differing concentrations of phosphorus-32 (³²P; 0.1 and 1 mGy d^-1), alone and in combination in marine (Mytilus galloprovincialis) and freshwater (Dreissena polymorpha) mussels. Genetic and molecular biomarkers were determined post-exposure and included DNA damage (as measured by the comet assay), micronuclei (MN) formation, γ-H2AX foci induction and the expression of key stress-related genes (i.e. hsp70/90, sod, cat, gst).

RESULTS

Overall, using a tissue-specific (i.e. gill and digestive gland) approach, genotoxic response was reflective of exposures where Cu had a slight additive effect on ³²P-induced damage across the species (but not all), cell types and dose rates. Multivariate analysis found significant correlations between comet and γ-H2AX assays, across both the tissues. Transcriptional expression of selected genes were generally unaltered in response to contaminant exposures, independent of species or tissues.

CONCLUSIONS

Our study is the first to explore the interactive effects of ionizing radiation (IR) and Cu on two bivalve species representing two ecological habitats. The complexity of IR-metal interactions demonstrate that extrapolation of findings obtained from single stressor studies into field conditions could be misrepresentative of real-world environments. In turn, environmental protective strategies deemed suitable in protecting biota from a single, isolated stressor may not be wholly adequate.

The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscus

The hard-shelled mussel (Mytilus coruscus) is an economically important shellfish that has been cultivated for the last decade. Due to over-exploitation, most mussel stocks have dramatically declined. Efforts to study this species' natural distribution, genetics, breeding, and cultivation have been hindered by the lack of a high-quality reference genome. To address this, we produced a hybrid high-quality reference genome of M. coruscus using a long-read platform to assemble the genome and short-read, high-quality technology to accurately correct for sequence errors. The genome was assembled into 10,484 scaffolds, a total length of 1.90 Gb, and a scaffold N50 of 898 kb. Ab initio annotation of the M. coruscus genome assembly identified a total of 42,684 genes. This accurate reference genome of M. coruscus provides an essential resource with the advantage of enabling the genome-scale selective breeding of M. coruscus. More importantly, it will also help in deciphering the speciation and local adaptation of the Mytilus species.

Whole-transcriptome sequencing (RNA-seq) analyses of the zebrafish liver cell line, ZFL, after acute exposure to Cu2+ ions

All cells require Cu as a cofactor, but Cu²⁺ induces toxicity and oxidative damage. A strict system is thus needed to maintain Cu homeostasis.

Transcriptome profiling reveals candidate flavonol-related genes of Tetrastigma hemsleyanum under cold stress

Background

Tetrastigma hemsleyanum Diels et Gilg is a valuable medicinal herb, whose main bioactive constituents are flavonoids. Chilling sensitivity is the dominant environmental factor limiting growth and development of the plants. But the mechanisms of cold sensitivity in this plant are still unclear. Also, not enough information on genes involved in flavonoid biosynthesis in T. hemsleyanum is available to understand the mechanisms of its physiological and pharmaceutical effects.

Results

The electrolyte leakage, POD activity, soluble protein, and MDA content showed a linear sustained increase under cold stress. The critical period of cold damage in T. hemsleyanum was from 12 h to 48 h. Expression profiles revealed 18,104 differentially expressed genes (DEGs) among these critical time points. Most of the cold regulated DEGs were early-response genes. A total of 114 unigenes were assigned to the flavonoid biosynthetic pathway. Fourteen genes most likely to encode flavonoid biosynthetic enzymes were identified. Flavonols of T. hemsleyanum might play a crucial role in combating cold stress. Genes encoding PAL, 4CL, CHS, ANR, FLS, and LAR were significantly up-regulated by cold stress, which could result in a significant increase in crucial flavonols (catechin, epicatechin, rutin, and quercetin) in T. hemsleyanum.

Conclusions

Overall, our results show that the expression of genes related to flavonol biosynthesis as well as flavonol content increased in T. hemsleyanum under cold stress. These findings provide valuable information regarding the transcriptome changes in response to cold stress and give a clue for identifying candidate genes as promising targets that could be used for improving cold tolerance via molecular breeding. The study also provides candidate genes involved in flavonoid biosynthesis and may be useful for clarifying the biosynthetic pathway of flavonoids in T. hemsleyanum.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6045-y) contains supplementary material, which is available to authorized users.

Long-term effect of water diversion and CSOs on the remediation of heavy metals and microbial community in river sediments

Untreated combined sewer overflows (CSOs) cause serious water pollution problems. In this study, the effects of CSO-induced heavy metals and the remediation practice of installation of a long-term water diversion (LTWD) on the microbial environment in river sediments were analyzed in an inland river. The Zn, Cd, Cr, and Cu contents in sediments and water were analyzed. DNA extraction and polymerase chain reaction analysis were conducted based on the Illumina MiSeq platform. The results showed that CSOs have a significant adverse impact on the diversity of microbial populations in river sediments. The LTWD is helpful in improving the richness of microorganisms and the proportion of Gram -ves, but it is challenging to reduce the accumulation of heavy metals in the sediment. The correlation analysis shows a strong relationship between some metabolic pathways and Zn and Cd accumulation in river sediments. Some detoxification compound metabolisms are also promoted at these sites. Thus, chronic exposure to environmental heavy metals from CSOs decreases the river microbial community, and further affects the ecological environment of the river. Therefore, without eliminating CSOs or reducing overflow frequency, it is difficult to alleviate the accumulation of heavy metals in river sediments and improve river ecology via water diversion alone.

Multiple Transcriptional Mechanisms Collectively Mediate Copper Resistance in Cupriavidus gilardii CR3

Bacteria resist copper (Cu) stress by implementing several metabolic mechanisms. However, these mechanisms are not fully understood. We investigated the mechanism of Cu resistance in Cupriavidus gilardii CR3, a Cu-resistant bacterium with a fully sequenced, annotated genome. The growth of CR3 was inhibited by higher Cu concentrations (≥1.0 mM) but not by lower ones (≤0.5 mM). CR3 accumulated Cu intracellularly (ratios of intercellular to extracellular Cu were 11.6, 4.24, and 3.9 in 0.1, 0.5, and 1.5 mM Cu treatments, respectively). A comparative transcriptome analysis of CR3 respectively revealed 310 and 413 differentially expressed genes under 0.5 and 1.5 mM Cu stress, most of which were up-regulated under Cu treatment. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analyses uncovered several genotype-specific biological processes related to Cu stress. Besides revealing known Cu resistance-related genes, our global transcriptomics approach indicated that sulfur metabolism, iron-sulfur cluster, and cell secretion systems are involved in mediating Cu resistance in strain CR3. These results suggest that bacteria collectively use multiple systems to cope with Cu stress. Our findings concerning the global transcriptome response to Cu stress in CR3 provide new information for understanding the intricate regulatory network of Cu homeostasis in prokaryotes.

Transcriptome-wide identification of differentially expressed genes in Procambarus clarkii in response to chromium challenge

Because of the high protein content and rich meat quality of crayfish Procambarus clarkii, it has become widely popular in China in recent years and has a high economic value. When P. clarkii is stimulated by heavy metals, it reacts to oxidation. P. clarkii has evolved antioxidant defense systems, including antioxidant enzymes such as catalase (CAT). The hexavalent form of Cr (VI) is a pathogenic factor that is of particular concern in aqueous systems because of its great toxicity to living organisms. In this study, we characterized the transcriptome of P. clarkii using a RNA sequencing method and performed a comparison between K₂Cr₂O₇-treated samples and controls. In total, 34,237 unigenes were annotated. We identified 5098 significantly differentially expressed genes (DEGs), including 2536 and 2562 were significantly up-regulated and down-regulated, respectively. In addition, quantitative real time-PCR (qRT-PCR) confirmed the up-regulation of a random selection of DEGs. Our results contribute to a more comprehensive understanding of the antioxidant defense system used by P. clarkii in response to heavy metal stress.

Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes

In molluscs, the shell secreted by mantle tissue during the biomineralization process is the first barrier against predators and mechanical damage. Changing environmental conditions, such as ocean acidification, influence shell strength and thus protection of the soft body within. Mussels are marine bivalves with important commercial and ecological value worldwide. Despite this importance, the proteins involved in the biomineralization and pigmentation processes in Mytilus spp. remain unclear, as does taxonomy of Mytilus taxa, though there have been many molecular studies. To further understanding in these areas, this study aimed to characterize and compare mantle transcriptomes of four mussel taxa using next generation sequencing. Mussels representing four taxa, were collected from several localities and RNA from mantle tissue was extracted. RNA sequences obtained were assembled, annotated and potential molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were identified. Candidate contigs putatively related to biomineralization and pigmentation processes were then selected and several transcripts were chosen for phylogenetic analyses from the Bivalvia class. Transcriptome comparisons between Mytilus taxa, including gene ontology (GO) enrichment analysis and orthologues identification were performed. Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Potential SSRs (483) and SNPs (1,497) were identified. Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis. Phylogenetic analyses of α-carbonic anhydrase, chitinase and tyrosinase revealed complex evolutionary history and diversity of these genes, which may be a result of duplication events or adaptation to different environments in mussels and other bivalves. Enrichment analyses revealed GO terms associated with pH and thermal response in Mytilus edulis from the North Sea and M. galloprovincialis from the Mediterranean Sea. The phylogenetic analysis within the genus Mytilus revealed M. californianus and M. coruscus to be genetically more distant from the other taxa: M. trossulus, M. edulis, M. chilensis and M. galloprovincialis. This work represents the first mantle transcriptome comparison between Mytilus taxa and provides contigs putatively involved in biomineralization.

Tissue-specific molecular and cellular toxicity of Pb in the oyster (Crassostrea gigas): mRNA expression and physiological studies

Lead (Pb) is one of the ubiquitous and toxic elements in aquatic environment. In oysters, gills and digestive glands are the main target organs for Pb-induced toxicity, but there is limited information on the molecular mechanisms underlying its toxicity. The present study investigated the Pb-induced toxicity mechanisms in the Pacific oyster (Crassostrea gigas) based on transcriptome, phenotypic anchoring, and validation of targeted gene expression. Gene ontology and pathway enrichment analyses revealed the differential Pb toxicity mechanisms in the tissues. In the gills, Pb disturbed the protein metabolism, with the most significant enrichment of the "protein processing in endoplasmic reticulum" pathway. The main mechanism comprised of a Pb-stimulated calcium (Ca²⁺) increase by the up-regulation of transporter-Ca-ATPase expression. The disturbed Ca²⁺ homeostasis then further induced high expressions of endoplasmic reticulum (ER) chaperones, leading to ER stress in the oysters. Unfolded proteins induced ER associated degradation (ERAD), thereby preventing the accumulation of folding-incompetent glycoproteins. However, Pb mainly induced oxidative reduction reactions in the digestive gland with high accumulation of lipid peroxidation products and high expression of antioxidant enzymes. Further, Pb induced fatty acid β-oxidation and CYP450 catalyzed ω-oxidation due to increased metabolic expenditure for detoxification. The increased content of arachidonic acid indicated that Pb exposure might alter unsaturated fatty acid composition and disturb cellular membrane functions. Taken together, our results provided a new insight into the molecular mechanisms underlying Pb toxicity in oysters.

Transcriptome Analysis of Hepatopancreas from the Cr (VI)-Stimulated Mantis Shrimp ( Oratosquilla oratoria) by Illumina Paired-End Sequencing: Assembly, Annotation, and Expression Analysis

Cr (VI), the pathogenicity factor, is widely known to cause toxic effects in living organisms. Given the economic importance of the mantis shrimp ( Oratosquilla oratoria), the understanding of impacts by Cr (VI) is considered important. In this study, transcriptome of mantis shrimp was characterized by a comparison between control and Cr (VI)-treated samples using RNA-seq approach. Totally, 88 234 826 bp and 13.24G clean reads were obtained. The total length and number of unigenes were 68 411 206 bp and 100 918, respectively. The maximal and average length of unigenes was 24 906 bp and 678 bp, respectively (N50, 798 bp). 7115 of these unigenes accounted for 7.05% of the total that were annotated in all databases. After annotation of assembled unigenes, 35 619 of them were assigned into 3 functional categories and 56 subcategories using Gene Ontology; 18 580 of them were assigned into 26 functional categories using Clusters of Orthologous Groups of proteins; 16 864 of them were assigned into 5 major categories and 32 subclasses using KEGG. Finally, 1730 genes were differentially expressed (DGEs), 9 up-regulated pathways (protein digestion and absorption, neuroactive ligand-receptor interaction, pancreatic secretion, tyrosine metabolism, amoebiasis, ECM-receptor interaction, riboflavin metabolism, amino sugar and nucleotide sugar metabolism and AGE-RAGE signaling pathway in diabetic complications) were significantly enriched ( q < 0.05), and one down-regulated pathway ( Staphylococcus aureus infection) was significantly enriched ( q < 0.05). Up-regulation of genes in pathways of protein digestion/absorption ( PepT1/SLC15A and ATP1B) and environment information processing ( COL1AS, COL4A; LAMA3_5, LAMB3; FN1 and TN) may imply the potentially positive toxicity resistance mechanisms.

Functional and molecular responses of the blue mussel Mytilus edulis' hemocytes exposed to cadmium - An in vitro model and transcriptomic approach

The bivalve mollusk, Mytilus edulis, is used as a sentinel species in several monitoring programs due to its ability to bio-accumulate contaminants. Its immune system consists of hemocytes and humoral components, which constitute the main part of the hemolymph. The present study is aimed at understanding the effects of Cd on the differentially expressed genes involved in the phagocytosis of M. edulis' hemocytes. Our approach focuses on an in vitro model by exposing hemocytes to different concentrations of Cd ranging from 10^-9 M to 10^-3 M. Phagocytosis and cell viability as functional markers were measured using flow cytometry. The molecular mechanisms regulated by Cd were investigated using RNA-seq and DGE analysis. Results showed that viability and phagocytosis of hemocytes exposed to 10^-3 M of Cd were significantly decreased after 21 h of exposure. RNA sequencing data showed that 1112 transcripts (out of 352,976 contigs) were differentially regulated by the highest concentration of Cd. Among these identified transcripts, 1028 and 84 were up and down-regulated respectively. The induction of super oxide dismutase (SOD), glutathion-s-transferase (GST), cytochrome P450 2C8 (CYP2C8), multidrug resistance protein (MRP1) and heat shock protein 70 (HSP70) suggests that Cd can regulate key molecular mechanisms. In addition, several toll-like receptors (TLR) as well as genes involved in phagocytosis (actin and CDC42) and apoptosis (caspase 8 and XIAP/IAP) were induced by Cd. Thus, our model highlights the effect of Cd on the phagocytic function of M. edulis' hemocytes along with the regulation of gene expression involved in innate immunity, detoxification and apoptosis. Further investigations need to be pursued to unravel the effects of Cd on the molecular mechanisms identified in this study.