Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors

Transcriptomic insights into cessation of clam embryonic development following transgenerational exposure to ocean acidity extreme

Ocean acidity extremes (OAX) events are becoming more frequent and intense in coastal areas in the context of climate change, generating widespread consequences on marine calcifying organisms and ecosystems they support. While transgenerational exposure to end-of-century scenario of ocean acidification (i.e., at pH 7.7) can confer calcifiers resilience, whether and to what extent such resilience holds true under OAX conditions is still poorly understood. Here, we found that transgenerational exposure of Ruditapes philippinarum to OAX resulted in cessation of embryonic development at the trochophore stage, implying devastating consequences of OAX on marine bivalves. We identified a large number of differentially expressed genes in embryos following transgenerationally exposed to OAX, which were mainly significantly enriched in KEGG pathways related to energy metabolism, immunity and apoptosis. These pathways were significantly activated, and genes involved in these processes were up-regulated, indicating strong cellular stress responses to OAX. These findings demonstrate that transgenerational exposure to OAX can result in embryonic developmental cessation by severe cellular damages, implying that transgenerational acclimation maybe not a panacea for marine bivalves to cope with OAX, and hence urgent efforts are required to understand consequences of intensifying OAX events in coastal ecosystems.

Multistress Interplay: Time and Duration of Ocean Acidification Modulate the Toxicity of Mercury and Other Metals

The current understanding of multistress interplay assumes stresses occur in perfect synchrony, but this assumption is rarely met in the natural marine ecosystem. To understand the interplay between nonperfectly overlapped stresses in the ocean, we manipulated a multigenerational experiment (F0-F3) to explore how different temporal scenarios of ocean acidification will affect mercury toxicity in a marine copepod Pseudodiaptomus annandalei. We found that the scenario of past acidification aggravated mercury toxicity but current and persistent acidification mitigated its toxicity. We specifically performed a proteomics analysis for the copepods of F3. The results indicated that current and persistent acidification initiated the energy compensation for development and mercury efflux, whereas past acidification lacked the barrier of H+ and had dysfunction in the detoxification and efflux system, providing a mechanistic understanding of mercury toxicity under different acidification scenarios. Furthermore, we conducted a meta-analysis on marine animals, demonstrating that different acidification scenarios could alter the toxicity of several other metals, despite evidence from nonsynchronous scenarios remaining limited. Our study thus demonstrates that time and duration of ocean acidification modulate mercury toxicity in marine copepods and suggests that future studies should move beyond the oversimplified scenario of perfect synchrony in understanding multistress interaction.

"Omics" Techniques Used in Marine Biofouling Studies

Biofouling is the growth of organisms on wet surfaces. Biofouling includes micro- (bacteria and unicellular algae) and macrofouling (mussels, barnacles, tube worms, bryozoans, etc.) and is a major problem for industries. However, the settlement and growth of some biofouling species, like oysters and corals, can be desirable. Thus, it is important to understand the process of biofouling in detail. Modern "omic" techniques, such as metabolomics, metagenomics, transcriptomics, and proteomics, provide unique opportunities to study biofouling organisms and communities and investigate their metabolites and environmental interactions. In this review, we analyze the recent publications that employ metagenomic, metabolomic, and proteomic techniques for the investigation of biofouling and biofouling organisms. Specific emphasis is given to metagenomics, proteomics and publications using combinations of different "omics" techniques. Finally, this review presents the future outlook for the use of "omics" techniques in marine biofouling studies. Like all trans-disciplinary research, environmental "omics" is in its infancy and will advance rapidly as researchers develop the necessary expertise, theory, and technology.

Effects of tralopyril on histological, biochemical and molecular impacts in Pacific oyster, Crassostrea gigas

Recently, the toxic effects of tralopyril, as a new antifouling biocide, on aquatic organisms have aroused widespread attention about the potential toxicity. However, the mechanism of tralopyril on marine mollusks has not been elaborated clearly. In this study, the histological, biochemical and molecular impacts of tralopyril on adult Crassostrea gigas were investigated. The results indicated that the 96 h LC50 of tralopyril to adult Crassostrea gigas was 911 μg/L. After exposure to tralopyril (0, 40, 80 and 160 μg/L) for 6 days, the mantle mucus secretion coverage ratio of Crassostrea gigas was increased with a dose-dependent pattern. Catalase (CAT) activity was significantly increased, amylase (AMS) activity, acid phosphatase (ACP) activity and calcium ion (Ca²⁺) concentration significantly decreased. Meanwhile, integrated biomarker responses (IBR) index suggested that higher concentrations of tralopyril caused severer damage to Crassostrea gigas. In addition, the mRNA expression levels of biomineralization related genes in the mantle were significantly upregulated. Collectively, this study firstly revealed the histological, biochemical and molecular impacts of tralopyril exposure on adult Crassostrea gigas, which provided new insights for understanding the toxicity of tralopyril in marine mollusks.

Exacerbation of copper pollution toxicity from ocean acidification: A comparative analysis of two bivalve species with distinct sensitivities

In estuarine ecosystems, bivalves experience large pH fluctuations caused by the anthropogenic elevation of atmospheric CO₂ and Cu pollution. This study investigates whether Cu toxicity increases indiscriminately in two bivalve species from different estuarine habitats as a result of elevated Cu bioaccumulation in acidified seawater. This was carried out by evaluating the effects of Cu exposure on two bivalve species (clams and scallops) for 28 d, at a series of gradient pH levels (pH 8.1, 7.8, and 7.6). The results demonstrated an increase in the Cu content in the soft tissues of clams and scallops in acidified seawater. Cu toxicity increased under acidified seawater by affecting the molecular pathways, physiological function, biochemical responses, and health status of clams and scallops. An iTRAQ-based quantitative proteomic analysis showed increased protein turnover, disturbed cytoskeleton and signal transduction pathways, apoptosis, and suppressed energy metabolism pathways in the clams and scallops under joint exposure to ocean acidification and Cu. The integrated biomarker response results suggested that scallops were more sensitive to Cu toxicity and/or ocean acidification than clams. The proteomic results suggested that the increased energy metabolism and suppressed protein turnover rates may contribute to a higher resistivity to ocean acidification in clams than scallops. Overall, this study provides molecular insights into the distinct sensitivities between two bivalve species from different habitats under exposure to ocean acidification and/or Cu. The findings emphasize the aggravating impact of ocean acidification on Cu toxicity in clams and scallops. The results show that ocean acidification and copper pollution may reduce the long-term viability of clams and scallops, and lead to the degradation of estuarine ecosystems.

A proteomic analysis of the effect of ocean acidification on the haemocyte proteome of the South African abalone Haliotis midae

As a result of increasing CO₂ emissions and the prevalence of global climate change, ocean acidification (OA) is becoming more pervasive, affecting many trophic levels, particularly those that rely on succinctly balanced ocean chemistry. This ultimately threatens community structures, as well as the future sustainability of the fishing/aquaculture industry. Understanding the molecular stress response of key organisms will aid in predicting their future survivability under changing environmental conditions. This study sought to elucidate the molecular stress response of the South African abalone, Haliotis midae, an understudied organism with high economic value, utilising a high throughput iTRAQ-based proteomics methodology. Adult abalone were exposed to control (pH 7.9) and experimental (pH 7.5) conditions for 12, 72 and 168 h, following which protein was isolated from sampled haemocytes and subsequently processed. iTRAQ-labelled peptides were analysed using mass spectrometry, while an array of bioinformatics tools was utilised for analysing the proteomic data. COG analysis identified "Cytoskeleton", "Translation, ribosomal structure and biogenesis", "Post-translational modification, protein turnover, chaperones", and "Intracellular trafficking, secretion and vesicular transport" to be the most enriched functional classes, while statistical analysis identified a total of 33 up-regulated and 23 down-regulated effectors of OA stress in abalone. Several of the up-regulated proteins that were identified function in central metabolism (ENO1, PGK, DUOX1, GPD2), the stress/immune response (CAMKI, HSPA5/GRP78, MAPKI), and cytoskeleton, protein sorting and signal transduction (IQGAP1, MYO9B, TLN1, RDX, TCP-1/CCT, SNX6, CHMP1a, VPS13a). Protein-protein interactions were predicted using STRING DB, Cytoscape and Ingenuity Pathway Analysis, providing a model of the effects of OA on the H. midae haemocyte proteome. The data indicated that H. midae underwent a metabolic shift under OA conditions to utilize more energy-efficient mechanisms of ATP generation, while attempts at restoring haemocyte stabilisation and homeostasis were reflected by up-regulation of oxidative stress and cytoskeletal proteins. Our results support other molluscan studies that report a complex array of overlapping functions of both the stress and immune response systems. This interplay of the mounted stress and immune response is maintained and observed through the up-regulation of proteins involved in protein synthesis and turnover, as well as intracellular signalling and transport. The data presented in this study highlight the value of employing sensitive and robust -omics technologies for assessing the effects of changing environmental conditions on marine organisms.

The Marine Gastropod Crepidula fornicata Remains Resilient to Ocean Acidification Across Two Life History Stages

Rising atmospheric CO₂ reduces seawater pH causing ocean acidification (OA). Understanding how resilient marine organisms respond to OA may help predict how community dynamics will shift as CO₂ continues rising. The common slipper shell snail Crepidula fornicata is a marine gastropod native to eastern North America that has been a successful invader along the western European coastline and elsewhere. It has also been previously shown to be resilient to global change stressors. To examine the mechanisms underlying C. fornicata’s resilience to OA, we conducted two controlled laboratory experiments. First, we examined several phenotypes and genome-wide gene expression of C. fornicata in response to pH treatments (7.5, 7.6, and 8.0) throughout the larval stage and then tested how conditions experienced as larvae influenced juvenile stages (i.e., carry-over effects). Second, we examined genome-wide gene expression patterns of C. fornicata larvae in response to acute (4, 10, 24, and 48 h) pH treatment (7.5 and 8.0). Both C. fornicata larvae and juveniles exhibited resilience to OA and their gene expression responses highlight the role of transcriptome plasticity in this resilience. Larvae did not exhibit reduced growth under OA until they were at least 8 days old. These phenotypic effects were preceded by broad transcriptomic changes, which likely served as an acclimation mechanism for combating reduced pH conditions frequently experienced in littoral zones. Larvae reared in reduced pH conditions also took longer to become competent to metamorphose. In addition, while juvenile sizes at metamorphosis reflected larval rearing pH conditions, no carry-over effects on juvenile growth rates were observed. Transcriptomic analyses suggest increased metabolism under OA, which may indicate compensation in reduced pH environments. Transcriptomic analyses through time suggest that these energetic burdens experienced under OA eventually dissipate, allowing C. fornicata to reduce metabolic demands and acclimate to reduced pH. Carry-over effects from larval OA conditions were observed in juveniles; however, these effects were larger for more severe OA conditions and larvae reared in those conditions also demonstrated less transcriptome elasticity. This study highlights the importance of assessing the effects of OA across life history stages and demonstrates how transcriptomic plasticity may allow highly resilient organisms, like C. fornicata, to acclimate to reduced pH environments.

Projected near-future ocean acidification decreases mercury toxicity in marine copepods

Here, we examined the combinational effect of ocean acidification (OA) and mercury (Hg) in the planktonic copepod Pseudodiaptomus annandalei in cross-factored response to different pCO₂ (400, 800 μatm) and Hg (control, 1.0 and 2.5 μg/L) exposures for three generations (F0-F2), followed by single-generation recovery (F3) under clean condition. Several phenotypic traits and Hg accumulation were analyzed for F0-F3. Furthermore, shotgun-based quantitative proteomics was performed for F0 and F2. Our results showed that OA insignificantly influenced the traits. During F0-F2, combined exposure reduced Hg accumulation as compared with the counterpart Hg treatment, supporting the mitigating effect of OA on Hg toxicity in copepods. Proteomics analysis indicated that the copepods probably increased energy production/storage and stress response to ensure physiological resilience against OA. However, Hg induced many toxic events (e.g., energy depletion and degenerated organomorphogenesis/embryogenesis for F0; cell cycle arrest and detrimental stress-defense for F2), which were translated to the population-level adverse outcome, i.e., compromised growth/reproduction. Particularly, compensatory proteome response was identified (e.g., increased immune defense for F0; energetic compensation and enhanced embryogenesis for F2), accounting for a negative interaction between OA and Hg. Together, this study provides the molecular mechanisms behind the effects of OA and Hg pollution in marine copepods.

Season specific influence of projected ocean changes on the response to cadmium of stress-related genes in Mytilus galloprovincialis

Anthropogenic inputs of carbon dioxide in the atmosphere are driving ocean warming and acidification. The potential threat represented by these changes for marine species could be amplified in coastal areas, characterized by higher levels of pollutants. In addition, temperate organisms may exhibit a different seasonal tolerance to stressors influenced by fluctuations of environmental and physiological factors. In this study, Mediterranean mussels Mytilus galloprovincialis collected both in summer and winter were exposed to combinations of two temperatures (SST, seasonal surface temperature and SST+5 °C) and two levels of pH (8.20 and 7.40) in clean or cadmium contaminated seawater (20 μg/L Cd). mRNA levels of genes related to metal-induced stress response were investigated, including metallothionein mt-20, heat-shock protein hsp70, superoxide dismutase Cu/Zn-sod, catalase cat, glutathione peroxidase gpx1 and glutathione S-transferase gst-pi. To further elucidate if tissues with different physiological roles could exhibit different responsiveness, such analyses were carried out in digestive gland and in gills of exposed mussels. mt-20 mRNA increase after Cd-exposure was higher in the digestive gland than in the gills, with few modulations by temperature or pH only in the latter. Acidification, alone or in combination with other stressors, increased hsp70 mRNA, with seasonal- and tissue-specificities (higher in summer and in digestive gland). Among antioxidants, gpx1 mRNA was affected by Cd in both tissues and seasons, with further modulations due to pH and temperature variation tissue- and season-specific; in winter the combination of Cd, warming and acidification affected Cu/Zn-sod both in digestive gland and gills and cat only in gills, while weak seasonal variations were observed for gst-pi transcripts only in digestive gland. The overall results highlighted the importance of considering seasonality and responsiveness of different tissues to predict the effects of sudden changes in environmental parameters on responsiveness to and toxicity of chemicals in marine coastal organisms.

Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc

Background

Protein expression patterns underlie physiological processes and phenotypic differences including those occurring during early development. The Pacific oyster (Crassostrea gigas) undergoes a major phenotypic change in early development from free-swimming larval form to sessile benthic dweller while proliferating in environments with broad temperature ranges. Despite the economic and ecological importance of the species, physiological processes occurring throughout metamorphosis and the impact of temperature on these processes have not yet been mapped out.

Results

Towards this, we comprehensively characterized protein abundance patterns for 7978 proteins throughout metamorphosis in the Pacific oyster at different temperature regimes. We used a multi-statistical approach including principal component analysis, ANOVA-simultaneous component analysis, and hierarchical clustering coupled with functional enrichment analysis to characterize these data. We identified distinct sets of proteins with time-dependent abundances generally not affected by temperature. Over 12 days, adhesion and calcification related proteins acutely decreased, organogenesis and extracellular matrix related proteins gradually decreased, proteins related to signaling showed sinusoidal abundance patterns, and proteins related to metabolic and growth processes gradually increased. Contrastingly, different sets of proteins showed temperature-dependent abundance patterns with proteins related to immune response showing lower abundance and catabolic pro-growth processes showing higher abundance in animals reared at 29 °C relative to 23 °C.

Conclusion

Although time was a stronger driver than temperature of metamorphic proteome changes, temperature-induced proteome differences led to pro-growth physiology corresponding to larger oyster size at 29 °C, and to altered specific metamorphic processes and possible pathogen presence at 23 °C. These findings offer high resolution insight into why oysters may experience high mortality rates during this life transition in both field and culture settings. The proteome resource generated by this study provides data-driven guidance for future work on developmental changes in molluscs. Furthermore, the analytical approach taken here provides a foundation for effective shotgun proteomic analyses across a variety of taxa.

Transcriptome Analysis of the Nematode Caenorhabditis elegans in Acidic Stress Environments

Ocean acidification and acid rain, caused by modern industries' fossil fuel burning, lead to a decrease in the living environmental pH, which results in a series of negative effects on many organisms. However, the underlying mechanisms of animals' response to acidic pH stress are largely unknown. In this study, we used the nematode Caenorhabditis elegans as an animal model to explore the regulatory mechanisms of organisms' response to pH decline. Two major stress-responsive pathways were found through transcriptome analysis in acidic stress environments. First, when the pH dropped from 6.33 to 4.33, the worms responded to the pH stress by upregulation of the col, nas, and dpy genes, which are required for cuticle synthesis and structure integrity. Second, when the pH continued to decrease from 4.33, the metabolism of xenobiotics by cytochrome P450 pathway genes (cyp, gst, ugt, and ABC transporters) played a major role in protecting the nematodes from the toxic substances probably produced by the more acidic environment. At the same time, the slowing down of cuticle synthesis might be due to its insufficient protective ability. Moreover, the systematic regulation pattern we found in nematodes might also be applied to other invertebrate and vertebrate animals to survive in the changing pH environments. Thus, our data might lay the foundation to identify the master gene(s) responding and adapting to acidic pH stress in further studies, and might also provide new solutions to improve assessment and monitoring of ecological restoration outcomes, or generate novel genotypes via genome editing for restoring in challenging environments especially in the context of acidic stress through global climate change.

Sea urchin larvae show resilience to ocean acidification at the time of settlement and metamorphosis

Extensive research has shown that the early life stages of marine organisms are sensitive to ocean acidification (OA). Less is known, however, on whether larval settlement and metamorphosis may be affected, or by which mechanisms. These are key processes in the life cycle of most marine benthic organisms, since they mark the transition between the free swimming larval stage to benthic life. We investigated whether OA could affect the larval settlement success of the sea urchin Evechinus chloroticus, a key coastal species with ecological, economic and cultural importance in New Zealand. We performed four settlement experiments to test whether reduced seawater pH (ranging from 8.1 to 7.0, at an interval of ~0.2 pH units) alters larval settlement and metamorphosis success. Our results show that settlement success was not significantly reduced when the larvae were exposed to a range of reduced seawater pH treatments (8.1-7.0) at time of settlement (on direct effects). Similarly, when presented with crustose coralline algae (CCA) pre-conditioned in seawater pH of either pH 8.1 or 7.7 for 28 days, larval settlement success remained unaltered (on indirect effects). We conclude that competent larvae in this species are resilient to OA at time of settlement. Further research on a range of taxa that vary in settlement selectivity and behaviour is needed in order to fully understand the effects of OA on the life cycle of marine invertebrates and the consequences it might have for future coastal marine ecosystems.

Opsonic character of the plasma proteins in phagocytosis-dependent host response to bacterial infection in a marine invertebrate, Crassostrea gigas

Phagocytosis is an evolutionarily conserved immune response, whose efficiency is fundamentally coupled with opsonization of extracellular microbes. How marine mollusks cells recognize and selectively capture pathogens during phagocytosis to clear them is not completely understood. In this study, we observed that plasma is extremely effective for oyster hemocyte phagocytosis, so we investigated candidate proteins among plasma proteins with binding affinity for Vibrio parahaemolyticus in Pacific oyster (Crassostrea gigas) by subjecting them to mass spectroscopy analysis for protein identification and characterization, and address the complex regulatory network to engulf invaders. There were 620 identified proteins potentially associated with bacteria binding and phagocytosis which could be quantified. Our results showed that C1q and lectins identified in Pacific oyster plasma held binding ability to bacteria, clearly suggesting their potent to be opsonins. The dominant expressed plasma protein p1-CgC1q (Complement component 1q)-like protein was identified and its opsonic role was confirmed in this study. The cell surface receptor Cgintegrin interacts directly with p1-CgC1q to mediate phagocytosis. We further confirmed that the interaction between C1q and integrin not rely on the typical recognition site RGD but on the RGE. Evidence exist revealed that p1-CgC1q could coat bacteria via the endotoxin LPS (lipopolysaccharide) and subsequently bind the receptor integrin to significantly enhance hemocytic phagocytosis and bacteria clearance. This study has thus furnished clear evidence for the importance of plasma proteins in mollusk, shedding light on the humoral immunity and an underappreciated strategy in marine host-pathogen interactions.

Molecular adaptation of molluscan biomineralisation to high-CO2 oceans - The known and the unknown

High-CO₂ induced ocean acidification (OA) reduces the calcium carbonate (CaCO₃) saturation level (Ω) and the pH of oceans. Consequently, OA is causing a serious threat to several ecologically and economically important biomineralising molluscs. Biomineralisation is a highly controlled biochemical process by which molluscs deposit their calcareous structures. In this process, shell matrix proteins aid the nucleation, growth and assemblage of the CaCO₃ crystals in the shell. These molluscan shell proteins (MSPs) are, ultimately, responsible for determination of the diverse shell microstructures and mechanical strength. Recent studies have attempted to integrate gene and protein expression data of MSPs with shell structure and mechanical properties. These advances made in understanding the molecular mechanism of biomineralisation suggest that molluscs either succumb or adapt to OA stress. In this review, we discuss the fate of biomineralisation process in future high-CO₂ oceans and its ultimate impact on the mineralised shell's structure and mechanical properties from the perspectives of limited substrate availability theory, proton flux limitation model and the omega myth theory. Furthermore, studying the interplay of energy availability and differential gene expression is an essential first step towards understanding adaptation of molluscan biomineralisation to OA, because if there is a need to change gene expression under stressors, any living system would require more energy than usual. To conclude, we have listed, four important future research directions for molecular adaptation of molluscan biomineralisation in high-CO₂ oceans: 1) Including an energy budgeting factor while understanding differential gene expression of MSPs and ion transporters under OA. 2) Unraveling the genetic or epigenetic changes related to biomineralisation under stressors to help solving a bigger picture about future evolution of molluscs, and 3) Understanding Post Translational Modifications of MSPs with and without stressors. 4) Understanding carbon uptake mechanisms across taxa with and without OA to clarify the OA theories on Ω.

Ocean acidification promotes broad transcriptomic responses in marine metazoans: a literature survey

For nearly a decade, the metazoan-focused research community has explored the impacts of ocean acidification (OA) on marine animals, noting that changes in ocean chemistry can impact calcification, metabolism, acid-base regulation, stress response and behavior in organisms that hold high ecological and economic value. Because OA interacts with several key physiological processes in marine organisms, transcriptomics has become a widely-used method to characterize whole organism responses on a molecular level as well as inform mechanisms that explain changes in phenotypes observed in response to OA. In the past decade, there has been a notable rise in studies that examine transcriptomic responses to OA in marine metazoans, and here we attempt to summarize key findings across these studies. We find that organisms vary dramatically in their transcriptomic responses to pH although common patterns are often observed, including shifts in acid-base ion regulation, metabolic processes, calcification and stress response mechanisms. We also see a rise in transcriptomic studies examining organismal response to OA in a multi-stressor context, often reporting synergistic effects of OA and temperature. In addition, there is an increase in studies that use transcriptomics to examine the evolutionary potential of organisms to adapt to OA conditions in the future through population and transgenerational experiments. Overall, the literature reveals complex organismal responses to OA, in which some organisms will face more dramatic consequences than others. This will have wide-reaching impacts on ocean communities and ecosystems as a whole.

Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2

Pacific geoducks (Panopea generosa) are clams found along the northeast Pacific coast where they are important components of coastal and estuarine ecosystems and a major aquaculture product. The Pacific coastline, however, is also experiencing rapidly changing ocean habitat, including significant reductions in pH. To better understand the physiological impact of ocean acidification on geoduck clams, we characterized for the first time the proteomic profile of this bivalve during larval development and compared it to that of larvae exposed to low pH conditions. Geoduck larvae were reared at pH 7.5 (ambient) or pH 7.1 in a commercial shellfish hatchery from day 6 to day 19 postfertilization and sampled at six time points for an in-depth proteomics analysis using high-resolution data-dependent analysis. Larvae reared at low pH were smaller than those reared at ambient pH, especially in the prodissoconch II phase of development, and displayed a delay in their competency for settlement. Proteomic profiles revealed that metabolic, cell cycle, and protein turnover pathways differed between the two pH and suggested that differing phenotypic outcomes between pH 7.5 and 7.1 are likely due to environmental disruptions to the timing of physiological events. In summary, ocean acidification results in elevated energetic demand on geoduck larvae, resulting in delayed development and disruptions to normal molecular developmental pathways, such as carbohydrate metabolism, cell growth, and protein synthesis.

Effects of acidification on the proteome during early development of Babylonia areolata

Increases in atmospheric CO2 partial pressure have lowered seawater pH in marine ecosystems, a process called ocean acidification (OA). The effects of OA during the critical stages of larval development may have disastrous consequences for some marine species, including Babylonia areolata (Link 1807), a commercially important sea snail in China and South East Asia. To investigate how OA affects the proteome of Babylonia areolata, here we used label-free proteomics to study protein changes in response to acidified (pH 7.6) or ambient seawater (pH 8.1) during three larvae developmental stages of B. areolata, namely, the veliger larvae before attachment (E1), veliger larvae after attachment (E2), and carnivorous juvenile snail (E3). In total, we identified 720 proteins. This result suggested that acidification seriously affects late veliger stage after attachment (E2). Further examination of the roles of differentially expressed proteins, which include glutaredoxin, heat-shock protein 70, thioredoxin, catalase, cytochrome-c-oxidase, peroxiredoxin 6, troponin T, CaM kinase II alpha, proteasome subunit N3 and cathepsin L, will be important for understanding the molecular mechanisms underlying pH reduction.

Transgenerational Proteome Plasticity in Resilience of a Marine Copepod in Response to Environmentally Relevant Concentrations of Microplastics

Here, we examined the multigenerational effect of microplastics (6-μm polystyrene beads; with different environmentally relevant concentrations of 0.023 and 0.23 mg/L in seawater) on the marine copepod Tigriopus japonicus under two-generation exposure (F0-F1) followed by one-generation recovery (F2) in clean seawater. Also, the seven life-history traits (survival, sex ratio, developmental time of nauplius phase, developmental time to maturation, number of clutches, number of nauplii/clutch, and fecundity) were measured for each generation. Furthermore, to investigate within-generation proteomic response and transgenerational proteome plasticity, proteome profiling was conducted for the F1 and F2 copepods under the control and 0.23 mg/L microplastics treatment. The results showed successful ingestion of microplastics in F0-F1 under both exposure concentrations, while higher concentration (0.23 mg/L) of microplastics resulted in the significant reduction in survival rate, number of nauplii/clutch, and fecundity. However, the affected traits were totally restored in the recovery generation (F2). Proteomic analysis demonstrated that microplastics exposure increased several cellular biosynthesis processes and, in turn, reduced energy storage due to the trade-off, hence compromising survival and reproduction of the treated copepods in F1. Interestingly, the two-generational effect of microplastics in copepods had significant transgenerational proteome plasticity as demonstrated by increased energy metabolism and stress-related defense pathway, which accounts for regaining of the compromised phenotypic traits during recovery (i.e., F2). Overall, this study provides a molecular understanding on the effect of microplastics at a translational level under long-term multigenerational exposure in marine copepods, and also the transgenerational proteome plasticity is likely rendering the robustness of copepods in response to microplastics pollution.

Seawater acidification increases copper toxicity: A multi-biomarker approach with a key marine invertebrate, the Pacific Oyster Crassostrea gigas

Ocean acidification (OA) has been found to increase the release of free Cu²⁺ in seawater. However, only a handful of studies have investigated the influence of OA on Cu accumulation and cellular toxicity in bivalve species. In this study, Pacific oysters, Crassostrea gigas, were exposed to 25 μg/L Cu²⁺ at three pH levels (8.1, 7.8 and 7.6) for 14 and 28 days. Physiological and histopathological parameters [(clearance rate (CR), respiration rate (RR), histopathological damage and condition index (CI)), oxidative stress and neurotoxicity biomarkers [superoxide dismutase (SOD) and glutathione transferase (GST) activities, lipid peroxidation (LPO) and acetylcholinesterase (AChE) activity], combined with glycolytic enzyme activities [pyruvate kinase (PK) and hexokinase (HK)] were investigated in C. gigas. The bioconcentration of Cu was increased in soft tissues of Cu-exposed oysters under OA. Our results suggest that both OA and Cu could lead to physiological disturbance, oxidative stress, cellular damage, disturbance in energy metabolism and neurotoxicity in oysters. The inhibited CR, increased glycolytic enzymes activities and decreased CI suggested that the energy metabolism strategy adopted by oysters was not sustainable in the long term. Furthermore, integrated biomarker response (IBR) results found that OA and Cu exposure lead to severe stress to oysters, and co-exposure was the most stressful condition. Results from this study highlight the need to include OA in future environmental assessments of pollutants and hazardous materials to better elucidate the risks of those environmental perturbations.

Understanding the transition from water to land: Insights from multi-omic analyses of the perivitelline fluid of apple snail eggs

Unlike most of the freshwater gastropod families, the family Ampullariidae includes members that exhibit both underwater and aerial oviposition, making it an ideal model for understanding mechanisms underlying the evolutionary transition from water to land. We applied SDS-PAGE and LC-MS/MS to analyse the proteome of the egg perivitelline fluid (PVF) of Marisa cornuarietis - an aquatic ovipositing ampullariid. Comparison with the reported PVF proteomes of two aerial ovipositing ampullariids (Pomacea canaliculata and P. maculata) showed that the three species all contain several major perivitellins that nourish the embryos. However, M. cornuarietis invests more heavily on immune-related proteins, which might be due to exposure to aquatic pathogens. Interestingly, only the PVF of out-of-water egg laying species have PV2 - a neurotoxin lethal to mice, and a calcium-binding protein which might be involved in the formation of calcareous eggshell. Integrated phylogenetic, evolutionary and gene expressional analyses detected the involvement of gene duplication, positive selection and neofunctionalisation in the formation of several major PVF proteins. Overall, our study provides multiple lines of evidence of adaptive evolution in the PVF proteins, and contributes to a better understanding of how aquatic gastropod ancestors invaded terrestrial habitats. SIGNIFICANCE: Aerial egg deposition has evolved in several groups of animals, but except for Vertebrata little is known about the mechanisms underlying this critical evolution process. We compared aquatic and aerial egg laying apple snails to understand the molecular mechanisms enabling such a transition in egg laying habitat. We found that the composition of perivitelline fluid proteomes of underwater and aerial egg depositors was remarkably different, and then gene duplication and positive selection were responsible for the formation of such novel proteins than enabled the evolutionary transition.

Seawater acidification aggravated cadmium toxicity in the oyster Crassostrea gigas: Metal bioaccumulation, subcellular distribution and multiple physiological responses

Mounting evidence has demonstrated the combined effects of ocean acidification (OA) and other environmental stressors on marine organisms. Although metal pollution is widely distributed in coasts and estuaries, the combined effects of OA and metal pollution have received little attention until recent years. In this study, the accumulation and subcellular distribution of cadmium (Cd) and the physiological responses of the oyster Crassostrea gigas were investigated after 31 days of exposure to OA and Cd, either alone or in combination. Increased Cd accumulation was found both in gills (about 57% increase at pH 7.8, 22% increase at pH 7.6) and digestive glands (about 38% increase at pH 7.8, 22% increase at pH 7.6) of C. gigas under elevated pCO₂ exposure. Although a similar total Cd accumulation pattern was seen in oyster gills and digestive glands, a higher partition of Cd in the BIM (biologically inactive metal) fractions of gills (about 60%) was found in Cd-exposed treatments compared to the digestive glands (about 45%), which might correspond to the generally lower toxicity in gills. Moreover, synergetic effects of Cd and OA on the oxidative stresses, histopathological damage, and apoptosis of exposed oysters were observed in this study, which might be explained by significant interactions of these two factors on increased generation of ROS. These findings demonstrated that OA could aggravate the toxicity of metals in marine organisms, with significant implications for coastal benthic ecosystems regarding the widespread metal contamination and the concurrent increase of acidified seawater.

Transcriptomics and Fitness Data Reveal Adaptive Plasticity of Thermal Tolerance in Oysters Inhabiting Different Tidal Zones

Fine-scale adaptive evolution is always constrained by strong gene flow at vertical level in marine organisms. Rapid environmental fluctuations and phenotypic plasticity through optimization of fitness-related traits in organisms play important roles in shaping intraspecific divergence. The coastal systems experience strong variations in multiple abiotic environmental factors, especially the temperature. We used a typical intertidal species, Pacific oyster (Crassostrea gigas), to investigate the interaction between plasticity and adaptive evolution. We collected intertidal and subtidal oysters from two ecological niches and carried out common garden experiments for one generation. We identified fine-scale vertical adaptive divergence between intertidal and subtidal F1 progeny at both sites, based on different hierarchical phenotypes, including morphological, physiological, and molecular traits. We further quantified the global plasticity to thermal stress through transcriptomic analysis. The intertidal oysters exhibited slow growth rate. However, they showed high survival and metabolic rates under heat stress, indicating vertically fine-scale phenotypic adaptive mechanisms and evolutionary trade-offs between growth and thermal tolerance. Transcriptomic analysis confirmed that the intertidal oysters have evolved high plasticity. The genes were classified into three types: evolutionarily divergent, concordantly plastic, and adaptive plastic genes. The evolved divergence between intertidal and subtidal oysters for these gene sets showed a significant positive correlation with plastic changes of subtidal populations in response to high temperature. Furthermore, the intertidal oysters exhibited delayed large-scale increase in expressional plasticity than that in subtidal counterparts. The same direction between plasticity and selection suggests that the oysters have evolved adaptive plasticity. This implies that adaptive plasticity facilitates the oyster to adapt to severe intertidal zones. The oysters exposed to strong environmental variability are thermal tolerant and have high adaptive potential to face the current global warming. Our findings will not only provide new insights into the significant role of plasticity in adaptive evolution that can be extended to other marine invertebrates, but also provide basic information for oyster resources conservation and reef reestablishment.

Seawater Acidification Reduced the Resistance of Crassostrea gigas to Vibrio splendidus Challenge: An Energy Metabolism Perspective

Negative physiological impacts induced by exposure to acidified seawater might sensitize marine organisms to future environmental stressors, such as disease outbreak. The goal of this study was to evaluate if ocean acidification (OA) could reduce the resistance capability of the Pacific oyster (Crassostrea gigas) to Vibrio splendidus challenge from an energy metabolism perspective. In this study, the Pacific oyster was exposed to OA (pH 7.6) for 28 days and then challenged by V. splendidus for another 72 h. Antioxidative responses, lipid peroxidation, metabolic (energy sensors, aerobic metabolism, and anaerobic metabolism) gene expression, glycolytic enzyme activity, and the content of energy reserves (glycogen and protein) were investigated to evaluate the environmental risk of pathogen infection under the condition of OA. Our results demonstrated that following the exposure to seawater acidification, oysters exhibited an energy modulation with slight inhibition of aerobic energy metabolism, stimulation of anaerobic metabolism, and increased glycolytic enzyme activity. However, the energy modulation ability and antioxidative regulation of oysters exposed to seawater acidification may be overwhelmed by a subsequent pathogen challenge, resulting in increased oxidative damage, decreased aerobic metabolism, stimulated anaerobic metabolism, and decreased energy reserves. Overall, although anaerobic metabolism was initiated to partially compensate for inhibited aerobic energy metabolism, increased oxidative damage combined with depleted energy reserves suggested that oysters were in an unsustainable bioenergetic state and were thereby incapable of supporting long-term population viability under conditions of seawater acidification and a pathogen challenge from V. splendidus.

Effects of ocean acidification on copepods

Ocean acidification (OA) leads to significant changes in seawater carbon chemistry, broadly affects marine organisms, and considered as a global threat to the fitness of marine ecosystems. Due to the crucial role of copepods in marine food webs of transferring energy from primary producers to higher trophic levels, numerous studies have been conducted to examine the impacts of OA on biological traits of copepods such as growth and reproduction. Under OA stress, the copepods demonstrated species-specific and stage-dependent responses. Notably, different populations of the same copepod species demonstrated different sensitivities to the increased pCO₂. In copepods, the deleterious effects of OA are also reinforced by other naturally occurring co-stressors (e.g., thermal stress, food deprivation, and metal pollution). Given that most OA stress studies have focused on the effects of short-term exposure (shorter than a single generation), experiments using adults might have underestimated the damaging effects of OA and the long-term multigenerational exposure to multiple stressors (e.g., increased pCO₂ and food shortage) will be required. Particularly, omics-based technologies (e.g., genomics, proteomics, and metabolomics) will be helpful to better understand the underlying processes behind biological responses (e.g., survival, development, and offspring production) at the mechanistic level which will improve our predictions of the responses of copepods to climate change stressors including OA.

Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms

Background

Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 h post fertilization, and it has been demonstrated that changes in water chemistry can cause delays in shell formation, shell deformations and higher mortality rates. In this study, we use the delay in shell formation associated with exposure to CO₂-acidified seawater to identify genes correlated with initial shell deposition.

Results

By fitting linear models to gene expression data in ambient and low aragonite saturation treatments, we are able to isolate 37 annotated genes correlated with initial larval shell formation, which can be categorized into 1) ion transporters, 2) shell matrix proteins and 3) protease inhibitors. Clustering of the gene expression data into co-expression networks further supports the result of the linear models, and also implies an important role of dynein motor proteins as transporters of cellular components during the initial shell formation process.

Conclusions

Using an RNA-Seq approach with high temporal resolution allows us to identify a conceptual model for how oyster larval calcification is initiated. This work provides a foundation for further studies on how genetic variation in these identified genes could affect fitness of oyster populations subjected to future environmental changes, such as ocean acidification.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4519-y) contains supplementary material, which is available to authorized users.

Tropical CO2 seeps reveal the impact of ocean acidification on coral reef invertebrate recruitment

Rising atmospheric CO₂ concentrations are causing ocean acidification by reducing seawater pH and carbonate saturation levels. Laboratory studies have demonstrated that many larval and juvenile marine invertebrates are vulnerable to these changes in surface ocean chemistry, but challenges remain in predicting effects at community and ecosystem levels. We investigated the effect of ocean acidification on invertebrate recruitment at two coral reef CO₂ seeps in Papua New Guinea. Invertebrate communities differed significantly between 'reference' (median pH7.97, 8.00), 'high CO₂' (median pH7.77, 7.79), and 'extreme CO₂' (median pH7.32, 7.68) conditions at each reef. There were also significant reductions in calcifying taxa, copepods and amphipods as CO₂ levels increased. The observed shifts in recruitment were comparable to those previously described in the Mediterranean, revealing an ecological mechanism by which shallow coastal systems are affected by near-future levels of ocean acidification.

Transcriptomic profiling of adaptive responses to ocean acidification

Some populations of marine organisms appear to have inherent tolerance or the capacity for acclimation to stressful environmental conditions, including those associated with climate change. Sydney rock oysters from the B2 breeding line exhibit resilience to ocean acidification (OA) at the physiological level. To understand the molecular basis of this physiological resilience, we analysed the gill transcriptome of B2 oysters that had been exposed to near-future projected ocean pH over two consecutive generations. Our results suggest that the distinctive performance of B2 oysters in the face of OA is mediated by the selective expression of genes involved in multiple cellular processes. Subsequent high-throughput qPCR revealed that some of these transcriptional changes are exclusive to B2 oysters and so may be associated with their resilience to OA. The intracellular processes mediated by the differentially abundant genes primarily involve control of the cell cycle and maintenance of cellular homeostasis. These changes may enable B2 oysters to prevent apoptosis resulting from oxidative damage or to alleviate the effects of apoptosis through regulation of the cell cycle. Comparative analysis of the OA conditioning effects across sequential generations supported the contention that B2 and wild-type oysters have different trajectories of changing gene expression and responding to OA. Our findings reveal the broad set of molecular processes underlying transgenerational conditioning and potential resilience to OA in a marine calcifier. Identifying the mechanisms of stress resilience can uncover the intracellular basis for these organisms to survive and thrive in a rapidly changing ocean.

Ocean acidification narrows the acute thermal and salinity tolerance of the Sydney rock oyster Saccostrea glomerata

Coastal and estuarine environments are characterised by acute changes in temperature and salinity. Organisms living within these environments are adapted to withstand such changes, yet near-future ocean acidification (OA) may challenge their physiological capacity to respond. We tested the impact of CO₂-induced OA on the acute thermal and salinity tolerance, energy metabolism and acid-base regulation capacity of the oyster Saccostrea glomerata. Adult S. glomerata were acclimated to three CO₂ levels (ambient 380μatm, moderate 856μatm, high 1500μatm) for 5weeks (24°C, salinity 34.6) before being exposed to a series of acute temperature (15-33°C) and salinity (34.2-20) treatments. Oysters acclimated to elevated CO₂ showed a significant metabolic depression and extracellular acidosis with acute exposure to elevated temperature and reduced salinity, especially at the highest CO₂ of 1500μatm. Our results suggest that the acute thermal and salinity tolerance of S. glomerata and thus its distribution will reduce as OA continues to worsen.

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2-acidified sea water

Ocean acidification is the increase in seawater pCO ₂ due to the uptake of atmospheric anthropogenic CO ₂, with the largest changes predicted to occur in the Arctic seas. For some marine organisms, this change in pCO ₂, and associated decrease in pH, represents a climate change-related stressor. In this study, we investigated the gene expression patterns of nauplii of the Arctic copepod Calanus glacialis cultured at low pH levels. We have previously shown that organismal-level performance (development, growth, respiration) of C. glacialis nauplii is unaffected by low pH. Here, we investigated the molecular-level response to lowered pH in order to elucidate the physiological processes involved in this tolerance. Nauplii from wild-caught C. glacialis were cultured at four pH levels (8.05, 7.9, 7.7, 7.5). At stage N6, mRNA was extracted and sequenced using RNA-seq. The physiological functionality of the proteins identified was categorized using Gene Ontology and KEGG pathways. We found that the expression of 151 contigs varied significantly with pH on a continuous scale (93% downregulated with decreasing pH). Gene set enrichment analysis revealed that, of the processes downregulated, many were components of the universal cellular stress response, including DNA repair, redox regulation, protein folding, and proteolysis. Sodium:proton antiporters were among the processes significantly upregulated, indicating that these ion pumps were involved in maintaining cellular pH homeostasis. C. glacialis significantly alters its gene expression at low pH, although they maintain normal larval development. Understanding what confers tolerance to some species will support our ability to predict the effects of future ocean acidification on marine organisms.

Temperature, energy metabolism, and adaptive divergence in two oyster subspecies

Comparisons of related species that have diverse spatial distributions provide an efficient way to investigate adaptive evolution in face of increasing global warming. The oyster subjected to high environmental selections is a model species as sessile marine invertebrate. This study aimed to detect the adaptive divergence of energy metabolism in two oyster subspecies from the genus Crassostrea—C. gigas gigas and C. gigas angulata—which are broadly distributed along the northern and southern coasts of China, respectively. We examined the effects of acute thermal stress on energy metabolism in two oyster subspecies after being common gardened for one generation in identical conditions. Thermal responses were assessed by incorporating physiological, molecular, and genomic approaches. Southern oysters exhibited higher fluctuations in metabolic rate, activities of key energetic enzymes, and levels of thermally induced gene expression than northern oysters. For genes involved in energy metabolism, the former displayed higher basal levels of gene expression and a more pronounced downregulation of thermally induced expression, while the later exhibited lower basal levels and a less pronounced downregulation of gene expression. Contrary expression pattern was observed in oxidative stress gene. Besides, energy metabolic tradeoffs were detected in both subspecies. Furthermore, the genetic divergence of a nonsynonymous SNP (SOD‐132) and five synonymous SNPs in other genes was identified and validated in these two subspecies, which possibly affects downstream functions and explains the aforementioned phenotypic variations. Our study demonstrates that differentiations in energy metabolism underlie the plasticity of adaptive divergence in two oyster subspecies and suggest C. gigas angulata with moderate phenotypic plasticity has higher adaptive potential to cope with exacerbated global warming.

Contrasting impacts of ocean acidification and warming on the molecular responses of CO2-resilient oysters

BACKGROUND

This study characterises the molecular processes altered by both elevated CO₂ and increasing temperature in oysters. Differences in resilience of marine organisms against the environmental stressors associated with climate change will have significant implications for the sustainability of coastal ecosystems worldwide. Some evidence suggests that climate change resilience can differ between populations within a species. B2 oysters represent a unique genetic resource because of their capacity to better withstand the impacts of elevated CO₂ at the physiological level, compared to non-selected oysters from the same species (Saccostrea glomerata). Here, we used proteomic and transcriptomic analysis of gill tissue to evaluate whether the differential response of B2 oysters to elevated CO₂ also extends to increased temperature.

RESULTS

Substantial and distinctive effects on protein concentrations and gene expression were evident among B2 oysters responding to elevated CO₂ or elevated temperature. The combination of both stressors also altered oyster gill proteomes and gene expression. However, the impacts of elevated CO₂ and temperature were not additive or synergistic, and may be antagonistic.

CONCLUSIONS

The data suggest that the simultaneous exposure of CO₂-resilient oysters to near-future projected ocean pH and temperature results in complex changes in molecular processes in order to prevent stress-induced cellular damage. The differential response of B2 oysters to the combined stressors also indicates that the addition of thermal stress may impair the resilience of these oysters to decreased pH. Overall, this study reveals the intracellular mechanisms that might enable marine calcifiers to endure the emergent, adverse seawater conditions resulting from climate change.

Global Proteome Profiling of a Marine Copepod and the Mitigating Effect of Ocean Acidification on Mercury Toxicity after Multigenerational Exposure

Previously, we found that ocean acidification (OA) mitigates mercury (Hg) toxicity to marine copepod Tigriopus japonicus under multigenerational exposure (four generations, F0-F3). To determine the response mechanisms of T. japonicus against long-term exposure to OA and Hg pollution, we investigated the proteome of F3 copepods after multigenerational exposure to four conditions: pCO₂ 400 μatm + control; pCO₂ 1000 μatm + control; pCO₂ 400 μatm +1.0 μg/L Hg; and pCO₂ 1000 μatm +1.0 μg/L Hg. Functional enrichment analysis indicated that OA enhanced the copepod's energy production mainly by increasing protein assimilation and proteolysis as a compensatory strategy, which explained its physiological resilience to reduced pH. Conversely, Hg treatment decreased many critical processes, including ferric iron binding, antioxidant activity, cellular homeostasis, and glutathione metabolism, and these toxic events could translate into higher-level responses, i.e., restrained reproduction in copepods. Importantly, the mediation of Hg toxicity in T. japonicus by OA could be explained by the enhanced lysosome-autophagy pathway proteomes that are responsible for repairing and removing damaged proteins and enzymes under stress. Overall, this study provided molecular insights into the response of T. japonicus to long-term exposure of OA and Hg, with a particular emphasis on the mitigating impact of the CO₂-driven acidification on Hg toxicity.

Evolutionary adaptation to environmental stressors: a common response at the proteomic level

Mechanistic trade-offs between traits under selection can shape and constrain evolutionary adaptation to environmental stressors. However, our knowledge of the quantitative and qualitative overlap in the molecular machinery among stress tolerance traits is highly restricted by the challenges of comparing and interpreting data between separate studies and laboratories, as well as to extrapolating between different levels of biological organization. We investigated the expression of the constitutive proteome (833 proteins) of 35 Drosophila melanogaster replicate populations artificially selected for increased resistance to six different environmental stressors. The evolved proteomes were significantly differentiated from replicated control lines. A targeted analysis of the constitutive proteomes revealed a regime-specific selection response among heat-shock proteins, which provides evidence that selection also adjusts the constitutive expression of these molecular chaperones. Although the selection response in some proteins was regime specific, the results were dominated by evidence for a "common stress response." With the exception of high temperature survival, we found no evidence for negative correlations between environmental stress resistance traits, meaning that evolutionary adaptation is not constrained by mechanistic trade-offs in regulation of functional important proteins. Instead, standing genetic variation and genetic trade-offs outside regulatory domains likely constrain the evolutionary responses in natural populations.