Transcriptomic profiling of adaptive responses to ocean acidification

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.

Exposure to virgin and marine incubated microparticles of biodegradable and conventional polymers modulates the hepatopancreas transcriptome of Mytilus galloprovincialis

Biodegradable polymers have been proposed as an alternative to conventional plastics to mitigate the impact of marine litter, but the research investigating their toxicity is still in its infancy. This study evaluates the potential ecotoxicological effects of both virgin and marine-incubated microparticles (MPs), at environmentally relevant concentration (0.1 mg/l), made of different biodegradable polymers (Polycaprolactone, Mater-Bi, cellulose) and conventional polymers (Polyethylene) on Mytilus galloprovincialis by using transcriptomics. This approach is increasingly being used to assess the effects of pollutants on organisms, obtaining data on numerous biological pathways simultaneously. Whole hepatopancreas de novo transcriptome sequencing was performed, individuating 972 genes differentially expressed across experimental groups compared to the control. Through the comparative transcriptomic profiling emerges that the preponderant effect is attributable to the marine incubation of MPs, especially for incubated polycaprolactone (731 DEGs). Mater-Bi and cellulose alter the smallest number of genes and biological processes in the mussel hepatopancreas. All microparticles, regardless of their polymeric composition, dysregulated innate immunity, and fatty acid metabolism biological processes. These findings highlight the necessity of considering the interactions of MPs with the environmental factors in the marine ecosystem when performing ecotoxicological evaluations. The results obtained contribute to fill current knowledge gaps regarding the potential environmental impacts of biodegradable polymers.

Molecular responses to ocean acidification in an Antarctic bivalve and an ascidian

Southern Ocean organisms are considered particularly vulnerable to Ocean acidification (OA), as they inhabit cold waters where calcite-aragonite saturation states are naturally low. It is also generally assumed that OA would affect calcifying animals more than non-calcifying animals. In this context, we aimed to study the impact of reduced pH on both types of species: the ascidian Cnemidocarpa verrucosa sp. A, and the bivalve Aequiyoldia eightsii, from an Antarctic fjord. We used gene expression profiling and enzyme activity to study the responses of these two Antarctic benthic species to OA. We report the results of an experiment lasting 66 days, comparing the molecular mechanisms underlying responses under two pCO2 treatments (ambient and elevated pCO2). We observed 224 up-regulated and 111 down-regulated genes (FC ≥ 2; p-value ≤ 0.05) in the ascidian. In particular, the decrease in pH caused an upregulation of genes involved in the immune system and antioxidant response. While fewer differentially expressed (DE) genes were observed in the infaunal bivalve, 34 genes were up-regulated, and 69 genes were downregulated (FC ≥ 2; p-value ≤ 0.05) in response to OA. We found downregulated genes involved in the oxidoreductase pathway (such as glucose dehydrogenase and trimethyl lysine dioxygenase), while the heat shock protein 70 was up-regulated. This work addresses the effect of OA in two common, widely distributed Antarctic species, showing striking results. Our major finding highlights the impact of OA on the non-calcifying species, a result that differ from the general trend, which describes a higher impact on calcifying species. This calls for discussion of potential effects on non-calcifying species, such as ascidians, a diverse and abundant group that form extended three-dimensional clusters in shallow waters and shelf areas in the Southern Ocean.

Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica)

Ocean acidification (OA) is a major stressor threatening marine calcifiers, including the eastern oyster (Crassostrea virginica). In this paper, we provide insight into the molecular mechanisms associated with resilience to OA, with the dual intentions of probing both acclimation and adaptation potential in this species. C. virginica were spawned, and larvae were reared in control or acidified conditions immediately after fertilization. RNA samples were collected from larvae and juveniles, and DNA samples were collected from juveniles after undergoing OA-induced mortality and used to contrast gene expression (RNAseq) and SNP (ddRADseq) profiles from animals reared under both conditions. Results showed convergence of evidence from both approaches, particularly in genes involved in biomineralization that displayed significant changes in variant frequencies and gene expression levels among juveniles that survived acidification as compared to controls. Downregulated genes were related to immune processes, supporting previous studies demonstrating a reduction in immunity from exposure to OA. Acclimation to OA via regulation of gene expression might confer short-term resilience to immediate threats; however, the costs may not be sustainable, underscoring the importance of selection of resilient genotypes. Here, we identified SNPs associated with survival under OA conditions, suggesting that this commercially and ecologically important species might have the genetic variation needed for adaptation to future acidification. The identification of genetic features associated with OA resilience is a highly-needed step for the development of marker-assisted selection of oyster stocks for aquaculture and restoration activities.

Molecular Features Associated with Resilience to Ocean Acidification in the Northern Quahog, Mercenaria mercenaria

The increasing concentration of CO₂ in the atmosphere and resulting flux into the oceans will further exacerbate acidification already threatening coastal marine ecosystems. The subsequent alterations in carbonate chemistry can have deleterious impacts on many economically and ecologically important species including the northern quahog (Mercenaria mercenaria). The accelerated pace of these changes requires an understanding of how or if species and populations will be able to acclimate or adapt to such swift environmental alterations. Thus far, studies have primarily focused on the physiological effects of ocean acidification (OA) on M. mercenaria, including reductions in growth and survival. However, the molecular mechanisms of resilience to OA in this species remains unclear. Clam gametes were fertilized under normal pCO₂ and reared under acidified (pH ~ 7.5, pCO₂ ~ 1200 ppm) or control (pH ~ 7.9, pCO₂ ~ 600 ppm) conditions before sampled at 2 days (larvae), 32 days (postsets), 5 and 10 months (juveniles) and submitted to RNA and DNA sequencing to evaluate alterations in gene expression and genetic variations. Results showed significant shift in gene expression profiles among clams reared in acidified conditions as compared to their respective controls. At 10 months of exposure, significant shifts in allele frequency of single nucleotide polymorphisms (SNPs) were identified. Both approaches highlighted genes coding for proteins related to shell formation, bicarbonate transport, cytoskeleton, immunity/stress, and metabolism, illustrating the role these pathways play in resilience to OA.

Epigenetic-associated phenotypic plasticity of the ocean acidification-acclimated edible oyster in the mariculture environment

For marine invertebrates with a pelagic-benthic life cycle, larval exposure to ocean acidification (OA) can affect adult performance in response to another environmental stressor. This carry-over effect has the potential to alter phenotypic traits. However, the molecular mechanisms that mediate "OA"-triggered carry-over effects have not been explored despite such information being key to improving species fitness and management strategies for aquafarming. This study integrated the genome-wide DNA methylome and transcriptome to examine epigenetic modification-mediated carry-over OA impacts on phenotypic traits of the ecologically and commercially important oyster species Crassostrea hongkongensis under field conditions. Larvae of C. hongkongensis were exposed to control pH 8.0 and low pH 7.4 conditions, mimicking near future OA scenario in their habitat, before being outplanted as post-metamorphic juveniles at two mariculture field sites with contrasting environmental stressors for 9 months. The larval carry-over OA effect was found to have persistent impacts on the growth and survival trade-off traits on the outplanted juveniles, although the beneficial or adverse effect depended on the environmental conditions at the outplanted sites. Site-specific plasticity was demonstrated with a diverse DNA methylation-associated gene expression profile, with signal transduction and the endocrine system being the most common and highly enriched functions. Highly methylated exons prevailed in the key genes related to general metabolic and endocytic responses and these genes are evolutionarily conserved in various marine invertebrates in response to OA. These results suggest that oysters with prior larval exposure history to OA had the ability to trigger rapid local adaptive responses via epigenetic modification to cope with multiple stressors in the field.

Is Ocean Acidification Really a Threat to Marine Calcifiers? A Systematic Review and Meta-Analysis of 980+ Studies Spanning Two Decades

Ocean acidification is considered detrimental to marine calcifiers, but mounting contradictory evidence suggests a need to revisit this concept. This systematic review and meta-analysis aim to critically re-evaluate the prevailing paradigm of negative effects of ocean acidification on calcifiers. Based on 5153 observations from 985 studies, many calcifiers (e.g., echinoderms, crustaceans, and cephalopods) are found to be tolerant to near-future ocean acidification (pH ≈ 7.8 by the year 2100), but coccolithophores, calcifying algae, and corals appear to be sensitive. Calcifiers are generally more sensitive at the larval stage than adult stage. Over 70% of the observations in growth and calcification are non-negative, implying the acclimation capacity of many calcifiers to ocean acidification. This capacity can be mediated by phenotypic plasticity (e.g., physiological, mineralogical, structural, and molecular adjustments), transgenerational plasticity, increased food availability, or species interactions. The results suggest that the impacts of ocean acidification on calcifiers are less deleterious than initially thought as their adaptability has been underestimated. Therefore, in the forthcoming era of ocean acidification research, it is advocated that studying how marine organisms persist is as important as studying how they perish, and that future hypotheses and experimental designs are not constrained within the paradigm of negative effects.

A Transcriptomic Analysis of Phenotypic Plasticity in Crassostrea virginica Larvae under Experimental Acidification

Ocean acidification (OA) is a major threat to marine calcifiers, and little is known regarding acclimation to OA in bivalves. This study combined physiological assays with next-generation sequencing to assess the potential for recovery from and acclimation to OA in the eastern oyster (Crassostrea virginica) and identify molecular mechanisms associated with resilience. In a reciprocal transplant experiment, larvae transplanted from elevated pCO₂ (~1400 ppm) to ambient pCO₂ (~350 ppm) demonstrated significantly lower mortality and larger size post-transplant than oysters remaining under elevated pCO₂ and had similar mortality compared to those remaining in ambient conditions. The recovery after transplantation to ambient conditions demonstrates the ability for larvae to rebound and suggests phenotypic plasticity and acclimation. Transcriptomic analysis supported this hypothesis as genes were differentially regulated under OA stress. Transcriptomic profiles of transplanted and non-transplanted larvae terminating in the same final pCO₂ converged, further supporting the idea that acclimation underlies resilience. The functions of differentially expressed genes included cell differentiation, development, biomineralization, ion exchange, and immunity. Results suggest acclimation as a mode of resilience to OA. In addition, the identification of genes associated with resilience can serve as a valuable resource for the aquaculture industry, as these could enable marker-assisted selection of OA-resilient stocks.

Acclimatory gene expression of primed clams enhances robustness to elevated pCO2

Sub-lethal exposure to environmental challenges may enhance ability to cope with chronic or repeated change, a process known as priming. In a previous study, pre-exposure to seawater enriched with pCO₂ improved growth and reduced antioxidant capacity of juvenile Pacific geoduck Panopea generosa, suggesting that transcriptional shifts may drive phenotypic modifications post-priming. To this end, juvenile clams were sampled and TagSeq gene expression data analyzed after 1) a 110-day acclimation under ambient (921 μatm, naïve) and moderately-elevated pCO₂ (2870 μatm, pre-exposed); then following 2) a second 7-day exposure to three pCO₂ treatments (ambient: 754 μatm; moderately-elevated: 2750 μatm; severely-elevated: 4940 μatm), a 7-day return to ambient pCO₂ , and a third 7-day exposure to two pCO₂ treatments (ambient: 967 μatm; moderately-elevated: 3030 μatm). Pre-exposed geoducks frontloaded genes for stress and apoptosis/innate immune response, homeostatic processes, protein degradation, and transcriptional modifiers. Pre-exposed geoducks were also responsive to subsequent encounters, with gene sets enriched for mitochondrial recycling and immune defense under elevated pCO₂ and energy metabolism and biosynthesis under ambient recovery. In contrast, gene sets with higher expression in naïve clams were enriched for fatty-acid degradation and glutathione components, suggesting naïve clams could be depleting endogenous fuels, with unsustainable energetic requirements if changes in carbonate chemistry persist. Collectively, our transcriptomic data indicates pCO₂ priming during post-larval periods could, via gene expression regulation, enhance robustness in bivalves to environmental change. Such priming approaches may be beneficial for aquaculture, as seafood demand intensifies concurrent with increasing climate change in marine systems.

Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification

Background

There is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like ocean acidification, are experienced by coastal ecosystems. Environmentally-induced changes to the methylome may regulate gene expression, but methylome responses can be species- and tissue-specific. Tissue-specificity has implications for gonad tissue, as gonad-specific methylation patterns may be inherited by offspring. We used the Pacific oyster (Crassostrea gigas) — a model for understanding pH impacts on bivalve molecular physiology due to its genomic resources and importance in global aquaculture— to assess how low pH could impact the gonad methylome. Oysters were exposed to either low pH (7.31 ± 0.02) or ambient pH (7.82 ± 0.02) conditions for 7 weeks. Whole genome bisulfite sequencing was used to identify methylated regions in female oyster gonad samples. C- > T single nucleotide polymorphisms were identified and removed to ensure accurate methylation characterization.

Results

Analysis of gonad methylomes revealed a total of 1284 differentially methylated loci (DML) found primarily in genes, with several genes containing multiple DML. Gene ontologies for genes containing DML were involved in development and stress response, suggesting methylation may promote gonad growth homeostasis in low pH conditions. Additionally, several of these genes were associated with cytoskeletal structure regulation, metabolism, and protein ubiquitination — commonly-observed responses to ocean acidification. Comparison of these DML with other Crassostrea spp. exposed to ocean acidification demonstrates that similar pathways, but not identical genes, are impacted by methylation.

Conclusions

Our work suggests DNA methylation may have a regulatory role in gonad and larval development, which would shape adult and offspring responses to low pH stress. Combined with existing molluscan methylome research, our work further supports the need for tissue- and species-specific studies to understand the potential regulatory role of DNA methylation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08781-5.

Intraspecific hybridization as a mitigation strategy of ocean acidification in marine bivalve noble scallop Chlamys nobilis

The driving factors of climate change, especially ocean acidification (OA), have many detrimental impacts on marine bivalves. Hybridization is one of the important methods to improve environmental tolerance of animals and plants. In this study, we explored the feasibility of intraspecific hybridization as an OA mitigation strategy in noble scallop Chlamys nobilis (ecologically and economically important bivalve species). The results of this study revealed that exposure of C. nobilis to OA condition significantly reduced the hatching rate, survival rate, growth rate (shell height, shell length, shell width and shell weight), and total carotenoid content (TCC), as well as increased the deformity rate of C. nobilis larvae. Interestingly, under both ambient water and OA condition, the intraspecific hybridization of C. nobilis exhibited heterosis in terms of hatching rate, survival rate and growth rate (excepted for growth in shell length under OA). Transcriptome sequencing of C. nobilis (inbreed and hybrid under ambient and OA conditions) identified four main differentially expressed genes involved in signal transduction, biological process maintenances, nucleic acid binding and post-translational modification. In addition, the expression of these four genes in hybrid C. nobilis was significantly higher than that in inbreed C. nobilis. In conclusion, hybrid C. nobilis showed heterosis in growth rate and survival rate under both ambient water and acidified seawater condition, which may be the result of enhanced expression of genes related to signal transduction, DNA replication and post-translational modification.

Synergistic Interaction of Low Salinity Stress With Vibrio Infection Causes Mass Mortalities in the Oyster by Inducing Host Microflora Imbalance and Immune Dysregulation

A sudden drop in salinity following extreme precipitation events usually causes mass mortality of oysters exposed to pathogens in ocean environment. While how low salinity stress interacts with pathogens to cause mass mortality remains obscure. In this study, we performed an experiment by low salinity stress and pathogen infection with Vibrio alginolyticus to investigate their synergistic effect on the mortality of the Pacific oyster toward understanding of the interaction among environment, host, and pathogen. We showed that low salinity stress did not significantly affect proliferation and virulence of V. alginolyticus, but significantly altered microbial composition and immune response of infected oysters. Microbial community profiling by 16S rRNA amplicon sequencing revealed disrupted homeostasis of digestive bacterial microbiota with the abundance of several pathogenic bacteria being increased, which may affect the pathogenesis in infected oysters. Transcriptome profiling of infected oysters revealed that a large number of genes associated with apoptosis and inflammation were significantly upregulated under low salinity, suggesting that low salinity stress may have triggered immune dysregulation in infected oysters. Our results suggest that host-pathogen interactions are strongly affected by low salinity stress, which is of great significance for assessing future environmental risk of pathogenic diseases, decoding the interaction among environment, host genetics and commensal microbes, and disease surveillance in the oyster.

Assessment of the juvenile vulnerability of symbiont-bearing giant clams to ocean acidification

Ocean acidification (OA) severely affects marine bivalves, especially their calcification processes. However, very little is known about the fate of symbiont-bearing giant clams in the acidified oceans, which hinders our ability to develop strategies to protect this ecologically and economically important group in coral reef ecosystems. Here, we explored the integrated juvenile responses of fluted giant clam Tridacna squamosa (Lamarck, 1819) to acidified seawater at different levels of biological organization. Our results revealed that OA did not cause a significant reduction in survival and shell growth performance, indicating that T. squamosa juveniles are tolerated to moderate acidification. Yet, significantly reduced net calcification rate demonstrated the calcifying physiology sensitivity to OA, in line with significant declines in symbiont photosynthetic yield and zooxanthellae density which in turn lowered the amount of energy supply for energetically expensive calcification processes. Subsequent transcriptome sequencing and comparative analysis of differentially expressed genes revealed that the regulation of calcification processes, such as transport of calcification substrates, acid-base regulation, synthesis of organic matrix in the calcifying fluid, as well as metabolic depression were the major response to OA. Taken together, the integration of physiological and molecular responses can provide a comprehensive understanding of how the early life history stages of giant clams respond to OA and make an important leap forward in assessing their fate under future ocean conditions.

The transcriptomic responses of blunt snout bream (Megalobrama amblycephala) to acute hypoxia stress alone, and in combination with bortezomib

BACKGROUND

Blunt snout bream (Megalobrama amblycephala) is sensitive to hypoxia. A new blunt snout bream strain, "Pujiang No.2", was developed to overcome this shortcoming. As a proteasome inhibitor, bortezomib (PS-341) has been shown to affect the adaptation of cells to a hypoxic environment. In the present study, bortezomib was used to explore the hypoxia adaptation mechanism of "Pujiang No.2". We examined how acute hypoxia alone (hypoxia-treated, HN: 1.0 mg·L^- 1), and in combination with bortezomib (hypoxia-bortezomib-treated, HB: Use 1 mg bortezomib for 1 kg fish), impacted the hepatic ultrastructure and transcriptome expression compared to control fish (normoxia-treated, NN).

RESULTS

Hypoxia tolerance was significantly decreased in the bortezomib-treated group (LOE_crit, loss of equilibrium, 1.11 mg·L^- 1 and 1.32 mg·L^- 1) compared to the control group (LOE_crit, 0.73 mg·L^- 1 and 0.85 mg·L^- 1). The HB group had more severe liver injury than the HN group. Specifically, the activities of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) in the HB group (52.16 U/gprot, 32 U/gprot) were significantly (p < 0.01) higher than those in the HN group (32.85 U/gprot, 21. 68 U/gprot). In addition, more severe liver damage such as vacuoles, nuclear atrophy, and nuclear lysis were observed in the HB group. RNA-seq was performed on livers from the HN, HB and NN groups. KEGG pathway analysis disclosed that many DEGs (differently expressed genes) were enriched in the HIF-1, FOXO, MAPK, PI3K-Akt and AMPK signaling pathway and their downstream.

CONCLUSION

We explored the adaptation mechanism of "Pujiang No.2" to hypoxia stress by using bortezomib, and combined with transcriptome analysis, accurately captured the genes related to hypoxia tolerance advantage.

Molecular mechanisms underlying responses of the Antarctic coral Malacobelemnon daytoni to ocean acidification

Benthic organisms of the Southern Ocean are particularly vulnerable to ocean acidification (OA), as they inhabit cold waters where calcite-aragonite saturation states are naturally low. OA most strongly affects animals with calcium carbonate skeletons or shells, such as corals and mollusks. We exposed the abundant cold-water coral Malacobelemnon daytoni from an Antarctic fjord to low pH seawater (LpH) (7.68 ± 0.17) to test its physiological responses to OA, at the level of gene expression (RT-PCR) and enzyme activity. Corals were exposed in short- (3 days) and long-term (54 days) experiments to two pCO₂ conditions (ambient and elevated pCO₂ equaling RCP 8.5, IPCC 2019, approximately 372.53 and 956.78 μatm, respectively). Of the eleven genes studied through RT-PCR, six were significantly upregulated compared with control in the short-term in the LpH condition, including the antioxidant enzyme superoxide dismutase (SOD), Heat Shock Protein 70 (HSP70), Toll-like receptor (TLR), galaxin and ferritin. After long-term exposure to low pH conditions, RT-PCR analysis showed seven genes were upregulated. These include the mannose-binding C-Lectin and HSP90. Also, the expression of TLR and galaxin, among others, continued to be upregulated after long-term exposure to LpH. Expression of carbonic anhydrase (CA), a key enzyme involved in calcification, was also significantly upregulated after long-term exposure. Our results indicated that, after two months, M. daytoni is not acclimatized to this experimental LpH condition. Gene expression profiles revealed molecular impacts that were not evident at the enzyme activity level. Consequently, understanding the molecular mechanisms behind the physiological processes in the response of a coral to LpH is critical to understanding the ability of polar species to cope with future environmental changes. Approaches integrating molecular tools into Antarctic ecological and/or conservation research make an essential contribution given the current ongoing OA processes.

Transgenerational plasticity responses of oysters to ocean acidification differ with habitat

Transgenerational plasticity (TGP) has been identified as a critical mechanism of acclimation that may buffer marine organisms against climate change, yet whether the TGP response of marine organisms is altered depending on their habitat is unknown. Many marine organisms are found in intertidal zones where they experience episodes of emersion (air exposure) daily as the tide rises and recedes. During episodes of emersion, the accumulation of metabolic carbon dioxide (CO2) leads to hypercapnia for many species. How this metabolic hypercapnia impacts the TGP response of marine organisms to climate change is unknown as all previous transgenerational studies have been done under subtidal conditions, where parents are constantly immersed. Here, we assess the capacity of the ecologically and economically important oyster, Saccostrea glomerata, to acclimate to elevated CO2 dependent on habitat, across its vertical distribution, from the subtidal to intertidal zone. Tidal habitat altered both the existing tolerance and transgenerational response of S. glomerata to elevated CO2. Overall, larvae from parents conditioned in an intertidal habitat had a greater existing tolerance to elevated CO2 than larvae from parents conditioned in a subtidal habitat, but had a lower capacity for beneficial TGP following parental exposure to elevated CO2. Our results suggest that the TGP responses of marine species will not be uniform across their distribution and highlights the need to consider the habitat of a species when assessing TGP responses to climate change stressors.

Separating the Wheat from the Chaff: The Use of Upstream Regulator Analysis to Identify True Differential Expression of Single Genes within Transcriptomic Datasets

The development of DNA microarray and RNA-sequencing technology has led to an explosion in the generation of transcriptomic differential expression data under a wide range of biologic systems including those recapitulating the monogenic muscular dystrophies. Data generation has increased exponentially due in large part to new platforms, improved cost-effectiveness, and processing speed. However, reproducibility and thus reliability of data remain a central issue, particularly when resource constraints limit experiments to single replicates. This was observed firsthand in a recent rare disease drug repurposing project involving RNA-seq-based transcriptomic profiling of primary cerebrocortical cultures incubated with clinic-ready blood-brain penetrant drugs. Given the low validation rates obtained for single differential expression genes, alternative approaches to identify with greater confidence genes that were truly differentially expressed in our dataset were explored. Here we outline a method for differential expression data analysis in the context of drug repurposing for rare diseases that incorporates the statistical rigour of the multigene analysis to bring greater predictive power in assessing individual gene modulation. Ingenuity Pathway Analysis upstream regulator analysis was applied to the differentially expressed genes from the Care4Rare Neuron Drug Screen transcriptomic database to identify three distinct signaling networks each perturbed by a different drug and involving a central upstream modulating protein: levothyroxine (DIO3), hydroxyurea (FOXM1), dexamethasone (PPARD). Differential expression of upstream regulator network related genes was next assessed in in vitro and in vivo systems by qPCR, revealing 5× and 10× increases in validation rates, respectively, when compared with our previous experience with individual genes in the dataset not associated with a network. The Ingenuity Pathway Analysis based gene prioritization may increase the predictive value of drug-gene interactions, especially in the context of assessing single-gene modulation in single-replicate experiments.

Comparative transcriptomic analysis for identification of candidate sex-related genes and pathways in Crimson seabream (Parargyrops edita)

Teleost fishes display the largest array of sex-determining systems among animals, resulting in various reproductive strategies. Research on sex-related genes in teleosts will broaden our understanding of the process, and provide important insight into the plasticity of the sex determination process in vertebrates in general. Crimson seabream (Parargyrops edita Tanaka, 1916) is one of the most valuable and abundant fish resources throughout Asia. However, little genomic information on P. edita is available. In the present study, the transcriptomes of male and female P. edita were sequenced with RNA-seq technology. A total of 388,683,472 reads were generated from the libraries. After filtering and assembling, a total of 79,775 non redundant unigenes were obtained with an N50 of 2,921 bp. The unigenes were annotated with multiple public databases, including NT (53,556, 67.13%), NR (54,092, 67.81%), Swiss-Prot (45,265, 56.74%), KOG (41,274, 51.74%), KEGG (46,302, 58.04%), and GO (11,056, 13.86%) databases. Comparison of the unigenes of different sexes of P. edita revealed that 11,676 unigenes (9,335 in females, 2,341 in males) were differentially expressed between males and females. Of these, 5,463 were specifically expressed in females, and 1,134 were specifically expressed in males. In addition, the expression levels of ten unigenes were confirmed to validate the transcriptomic data by qRT-PCR. Moreover, 34,473 simple sequence repeats (SSRs) were identified in SSR-containing sequences, and 50 loci were randomly selected for primer development. Of these, 36 loci were successfully amplified, and 19 loci were polymorphic. Finally, our comparative analysis identified many sex-related genes (zps, amh, gsdf, sox4, cyp19a, etc.) and pathways (MAPK signaling pathway, p53 signaling pathway, etc.) of P. edita. This informative transcriptomic analysis provides valuable data to increase genomic resources of P. edita. The results will be useful for clarifying the molecular mechanism of sex determination and for future functional analyses of sex-associated genes.

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.

Expected ocean warming conditions significantly alter the transcriptome of developing postlarval American lobsters (Homarus americanus): Implications for energetic trade-offs

The American lobster (Homarus americanus) is one of the most iconic and economically valuable fishery species in the Northwestern Atlantic. Surface ocean temperatures are rapidly increasing across much of the species' range, raising concern about resiliency in the face of environmental change. Warmer temperatures accelerate rates of larval development and enhance survival to the postlarval stage, but the potential costs at the molecular level have rarely been addressed. We explored how exposure to current summer temperatures (16 °C) or temperature regimes mimicking projected moderate or extreme warming scenarios (18 °C and 22 °C, respectively) for the Gulf of Maine during development influences the postlarval lobster transcriptome. After de novo assembling the transcriptome, we identified 2542 differentially expressed (DE; adjusted p < 0.05) transcripts in postlarvae exposed to 16 °C vs. 22 °C, and 422 DE transcripts in postlarvae reared at 16 °C vs. 18 °C. Lobsters reared at 16 °C significantly over-expressed transcripts related to cuticle formation and the immune response up to 14.4- and 8.5-fold respectively, relative to those reared at both 18 °C and 22 °C. In contrast, the expression of transcripts affiliated with metabolism increased up to 7.1-fold as treatment temperature increased. These results suggest that lobsters exposed to projected warming scenarios during development experience a shift in the transcriptome that reflects a potential trade-off between maintaining immune defenses and sustaining increased physiological rates under a warming environment. This could have major implications for post-settlement survival through increased risk of mortality due to disease and/or starvation if energetic demands cannot be met.

Diel-cycling seawater acidification and hypoxia impair the physiological and growth performance of marine mussels

Ocean acidification and hypoxia are concurrent in some coastal waters due to anthropogenic activities in the past decades. In the natural environment, pH and dissolved oxygen (DO) may fluctuate and follow diel-cycling patterns, but such effects on marine animals have not been comprehensively studied compared to their constant effects. In order to study the effects of diel-cycling seawater acidification and hypoxia on the fitness of marine bivalves, the thick shell mussels Mytilus coruscus were exposed to two constant levels of dissolved oxygen (2 mg/L, 8 mg/L) under two pH treatments (7.3, 8.1), as well as single diel fluctuating pH or DO, and the combined diel fluctuating of pH and DO for three weeks. The experimental results showed that constant acidification and hypoxia significantly reduced the extracellular pH (pH_e) and condition index (CI) of mussels, and significantly increased HCO₃^-, pCO₂ and standard metabolic rate (SMR). Diel fluctuating hypoxia and acidification also significantly reduced the pH_e and CI, and significantly increased pCO₂ and SMR, but had no significant effects on HCO₃^-. However, the diel-cycling acidification and hypoxia resulted in a higher CI compared to continuous exposure. In general, continuous and intermittent stress negatively impact the hemolymph and growth performance of mussels. However, mussels possess a little stronger resistance to diel-cycling seawater acidification and hypoxia than sustained stress.

Transgenerational acclimation to changes in ocean acidification in marine invertebrates

The rapid pace of increasing oceanic acidity poses a major threat to the fitness of the marine ecosystem, as well as the buffering capacity of the oceans. Disruption in chemical equilibrium in the ocean leads to decreased carbonate ion precipitation, resulting in calcium carbonate saturation. If these trends continue, calcifying invertebrates will experience difficultly maintaining their calcium carbonate exoskeleton and shells. Because malfunction of exoskeleton formation by calcifiers in response to ocean acidification (OA) will have non-canonical biological cascading results in the marine ecosystem, many studies have investigated the direct and indirect consequences of OA on ecosystem- and physiology-related traits of marine invertebrates. Considering that evolutionary adaptation to OA depends on the duration of OA effects, long-term exposure to OA stress over multi-generations may result in adaptive mechanisms that increase the potential fitness of marine invertebrates in response to OA. Transgenerational studies have the potential to elucidate the roles of acclimation, carryover effects, and evolutionary adaptation within and over generations in response to OA. In particular, understanding mechanisms of transgenerational responses (e.g., antioxidant responses, metabolic changes, epigenetic reprogramming) to changes in OA will enhance our understanding of marine invertebrate in response to rapid climate change.

Transgenerational biochemical effects of seawater acidification on the Manila clam (Ruditapes philippinarum)

Ocean acidification can negatively impact marine bivalves. Pivotal to projecting their fate is the ability to acclimate and adapt to shifts in seawater chemistry. Transgenerational plasticity enables marine bivalves to acclimate, yet the underlying mechanisms at different levels of biological organization remain poorly understood. Here, we performed a transgenerational experiment to understand biochemical responses of the Manila clam, Ruditapes philippinarum, following exposure to moderately reduced seawater pH (from 8.1 to 7.7). Activities of tissue calcification-relevant enzymes, such as carbonic anhydrase (CA), acid phosphatase (ACP) and alkaline phosphatase (ALP), energy-metabolizing enzymes, such as Na⁺/K⁺-ATPase (NKA) and Ca²⁺/Mg²⁺-ATPase (CMA), as well as tissue energy reserves (glycogen, lipid and protein) were assayed. With decreasing seawater pH, adult R. philippinarum exhibited significantly increased CA activity, and especially the clams with a history of transgenerational exposure displaying significantly higher CA activity than those spawned from parents exposed to ambient seawater pH. Yet, ACP and ALP activities remained unaffected. Transgenerational exposure to reduced seawater pH led to significant increases of NKA activity, while no transgenerational response of CMA activity was observed. Tissue glycogen and lipid contents were significantly depleted under acidified conditions regardless of transgenerational exposure. Yet, transgenerational alleviation in the net protein degradation was found. These findings suggest that our current understanding of transgenerational responses is still limited by the achievable time-window possible in the laboratory. While the energetic budget is lower under acidified conditions, there is no evidence of transgenerational recovery in term of energetic budget. Therefore, this work demonstrates that the critical basis of ocean acidification resilience can most likely be explained in energetic terms.

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.

Experimental acidification increases susceptibility of Mercenaria mercenaria to infection by Vibrio species

Ocean acidification alters seawater carbonate chemistry, which can have detrimental impacts for calcifying organisms such as bivalves. This study investigated the physiological cost of resilience to acidification in Mercenaria mercenaria, with a focus on overall immune performance following exposure to Vibrio spp. Larval and juvenile clams reared in seawater with high pCO₂ (~1200 ppm) displayed an enhanced susceptibility to bacterial pathogens. Higher susceptibility to infection in clams grown under acidified conditions was derived from a lower immunity to infection more so than an increase in growth of bacteria under high pCO₂. A reciprocal transplant of juvenile clams demonstrated the highest mortality amongst animals transplanted from low pCO₂/high pH to high pCO₂/low pH conditions and then exposed to bacterial pathogens. Collectively, these results suggest that increased pCO₂ will result in immunocompromised larvae and juveniles, which could have complex and pernicious effects on hard clam populations.

Antioxidant responses to seawater acidification in an invasive fouling mussel are alleviated by transgenerational acclimation

Ocean acidification and marine biofouling, which may interact in the future, pose two major threats to global coastal ecosystems. Yet, the fate of highly invasive fouling species in a rapidly acidifying ocean remains poorly understood, due to lack of information on multigenerational consequences at different levels of biological organization. Here, we investigated antioxidant responses of the mussel, Musculista senhousia, a swiftly spreading invasive fouling species in global coastal waters, following transgenerational exposure to elevated pCO₂. In the face of seawater acidification, M. senhousia without a prior history of transgenerational exposure to elevated pCO₂ showed resistance to lipid peroxidation, but significantly increased activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPx), indicated oxidative stress responses. However, enhanced transgenerational immunity occurred, as exemplified by observations that mussels originating from parents exposed to elevated pCO₂ exhibited significantly lower activities of SOD, CAT and GPx in comparison to those spawn from parents exposed to ambient pCO₂. Rapid transgenerational acclimation of M. senhousia in terms of reduced oxidative stress responses can likely be linked to the enhanced capacity of maintaining acid-base homeostasis previously demonstrated. These findings provide the first evidence of transgenerational plasticity at the biochemical level in highly invasive fouling bivalve species, and represent a step forward in understanding how they respond and acclimate in an acidifying ocean.

Selectively bred oysters can alter their biomineralization pathways, promoting resilience to environmental acidification

Commercial shellfish aquaculture is vulnerable to the impacts of ocean acidification driven by increasing carbon dioxide (CO₂ ) absorption by the ocean as well as to coastal acidification driven by land run off and rising sea level. These drivers of environmental acidification have deleterious effects on biomineralization. We investigated shell biomineralization of selectively bred and wild-type families of the Sydney rock oyster Saccostrea glomerata in a study of oysters being farmed in estuaries at aquaculture leases differing in environmental acidification. The contrasting estuarine pH regimes enabled us to determine the mechanisms of shell growth and the vulnerability of this species to contemporary environmental acidification. Determination of the source of carbon, the mechanism of carbon uptake and use of carbon in biomineral formation are key to understanding the vulnerability of shellfish aquaculture to contemporary and future environmental acidification. We, therefore, characterized the crystallography and carbon uptake in the shells of S. glomerata, resident in habitats subjected to coastal acidification, using high-resolution electron backscatter diffraction and carbon isotope analyses (as δ¹³ C). We show that oyster families selectively bred for fast growth and families selected for disease resistance can alter their mechanisms of calcite crystal biomineralization, promoting resilience to acidification. The responses of S. glomerata to acidification in their estuarine habitat provide key insights into mechanisms of mollusc shell growth under future climate change conditions. Importantly, we show that selective breeding in oysters is likely to be an important global mitigation strategy for sustainable shellfish aquaculture to withstand future climate-driven change to habitat acidification.

Assessing the impact of elevated pCO2 within and across generations in a highly invasive fouling mussel (Musculista senhousia)

Marine biofouling by the swiftly spreading invasive mussel (Musculista senhousia) has caused serious ecological and economic consequences in the global coastal waters. However, the fate of this highly invasive fouling species in a rapidly acidifying ocean remains unknown. Here, we demonstrated the impacts of ocean acidification within and across generations, to understand whether M. senhousia has the capacity to acclimate to changing ocean conditions. During the gonadal development, exposure of mussels to elevated pCO₂ caused significant decreases of survival, growth performance and condition index, and shifted the whole-organism energy budget by inflating energy expenses to fuel compensatory processes, eventually impairing the success of spawning. Yet, rapid transgenerational acclimation occurred during the early life history stage and persisted into adulthood. Eggs spawned from CO₂-exposed mussels were significantly bigger compared with those from non-CO₂-exposed mussels, indicating increased maternal provisioning into eggs and hence conferring larvae resilience under harsh conditions. Larvae with a prior history of transgenerational exposure to elevated pCO₂ developed faster and had a higher survival than those with no prior history of CO₂ exposure. Transgenerational exposure significantly increased the number of larvae completing metamorphosis. While significant differences in shell growth were no longer observed during juvenile nursery and adult grow-out, transgenerationally exposed mussels displayed improved survival in comparison to non-transgenerationally exposed mussels. Metabolic plasticity arose following transgenerational acclimation, generating more energy available for fitness-related functions. Overall, the present study demonstrates the remarkable ability of M. senhousia to respond plastically and acclimate rapidly to changing ocean conditions.

Immunotoxicity of four nanoparticles to a marine bivalve species, Tegillarca granosa

The increasing application of nanomaterials drives the unintentional release of nanoparticles (NPs) into the ocean, which may pose a potential threat to marine organisms. It has been demonstrated that exposure to NPs could chanllenge the immune responses of marine species. However, the affecting mechanism behind remains poorly understood. In this study, the immunotoxic impacts and the mechanisms underpinning the effects of four major NPs, including nZnO, nFe₂O₃, nCuO, and carbon nanotube (MWCNT), were investigated in blood clam, Tegillarca granosa. The results showed that exposure to tested NPs resulted in reduced total counts, altered cell composition, and constrained phagocytic activities of haemocytes. The intracellular contents of reactive oxygen species (ROS) and the degree of DNA damage of haemocytes were significantly induced, whereas the haemocyte viability was suppressed. Furthermore, NP exposures led to significant increases in the in vivo contents of neurotransmitters. Down-regulations of the immune- and neurotransmitter-related genes were detected as well. Our data suggest that NP exposures hampered the immune responses of blood clams most likely through (1) inducing ROS, causing DNA damage, and reducing cell viability of haemocytes, (2) altering the in vivo contents of neurotransmitters, and (3) affecting the expression of immune- and neurotransmitter-related genes.

Living in future ocean acidification, physiological adaptive responses of the immune system of sea urchins resident at a CO2 vent system

The effects of ocean acidification, a major anthropogenic impact on marine life, have been mainly investigated in laboratory/mesocosm experiments. We used the CO₂ vents at Ischia as a natural laboratory to study the long-term effects of ocean acidification on the sea urchin Paracentrotus lividus population resident in low-pH (7.8 ± 0.2) compared to that at two control sites (pH 8.02 ± 0.00; 8.02 ± 0.01). The novelty of the present study is the analysis of the sea urchin immune cells, the sentinels of environmental stress responses, by a wide-ranging approach, including cell morphology, biochemistry and proteomics. Immune cell proteomics showed that 311 proteins were differentially expressed in urchins across sites with a general shift towards antioxidant processes in the vent urchins. The vent urchin immune cells showed higher levels of total antioxidant capacity, up-regulation of phagosome and microsomal proteins, enzymes of ammonium metabolism, amino-acid degradation, and modulation of carbon metabolism proteins. Lipid-hydroperoxides and nitric oxide levels were not different in urchins from the different sites. No differences in the coelomic fluid pH, immune cell composition, animal respiration, nitrogen excretion and skeletal mineralogy were observed. Our results reveal the phenotypic plasticity of the immune system of sea urchins adapted to life at vent site, under conditions commensurate with near-future ocean acidification projections.

Impact of Ocean Acidification on the Energy Metabolism and Antioxidant Responses of the Yesso Scallop (Patinopecten yessoensis)

Ocean acidification (OA), which is caused by increasing levels of dissolved CO2 in the ocean, is a major threat to marine ecosystems. Multiple lines of scientific evidence show that marine bivalves, including scallops, are vulnerable to OA due to their poor capacities to regulate extracellular ions and acid-based status. However, the physiological mechanisms of scallops responding to OA are not well understood. In this study, we evaluated the effects of 45 days of exposure to OA (pH 7.5) on the energy metabolism and antioxidant capability of Yesso scallops. Some biochemical markers related to energy metabolism (e.g., content of glycogen and ATP, activity of ATPase, lactate dehydrogenase, glutamate oxaloacetate transaminase, and glutamate-pyruvate transaminase), antioxidant capacity (e.g., reactive oxygen species level, activity of superoxide dismutase, and catalase) and cellular damage (e.g., lipid peroxidation level) were measured. Our results demonstrate that the effects of the reduced pH (7.5) on scallops are varied in different tissues. The energy reserves are mainly accumulated in the adductor muscle and hepatopancreas. Yesso scallops exhibit energy modulation by increasing lactate dehydrogenase activities to stimulate anaerobic metabolism. The highly active Na+/K+-ATPase and massive ATP consumption in the mantle and gill indicate that a large amount of energy was allocated for the ion regulation process to maintain the acid-base balance in the reduced-pH environment. Moreover, the increase in the reactive oxygen species level and the superoxide dismutase and catalase activities in the gill and adductor muscle, indicate that oxidative stress was induced after long-term exposure to the reduced-pH environment. Our findings indicate that the effects of OA are tissue-specific, and physiological homeostasis could be modulated through different mechanisms for Yesso scallops.

Comparative De Novo transcriptome analysis of the Australian black-lip and Sydney rock oysters reveals expansion of repetitive elements in Saccostrea genomes

Ostreid oysters (the 'true oysters') represent a large and commercially important family of bivalve molluscs. Several species, such as the Pacific oyster (Magallana gigas), the American oyster (Crassostrea virginica), the European oyster (Ostrea edulis) and the Sydney rock oyster (Saccostrea glomerata), are currently farmed at a large scale. However a number of other species may also be suitable for commercial-scale aquaculture. One such species is the 'black-lip oyster', a large Saccostrea species of uncertain taxonomic affinity found in northern Australia. Here, phylogenetic analysis of the COI gene places this oyster within a clade identified in a previous study of Japanese Saccostrea species, 'Saccostrea lineage J'. To facilitate comparisons between this oyster and the better-studied S. glomerata, de novo transcriptomes were generated from larval stages and adult tissues of both species. Patterns of orthology indicated an expansion of repetitive elements within Saccostrea genomes when compared to M. gigas and C. virginica, which may be reflected in increased evolutionary rates and/or genome sizes. The generation of high-quality transcriptomes for these two commercially relevant oysters provides a valuable resource for gene identification and comparison of molecular processes in these and other mollusc species.

Ocean Acidification Affects the Cytoskeleton, Lysozymes, and Nitric Oxide of Hemocytes: A Possible Explanation for the Hampered Phagocytosis in Blood Clams, Tegillarca granosa

An enormous amount of anthropogenic carbon dioxide (CO₂) has been dissolved into the ocean, leading to a lower pH and changes in the chemical properties of seawater, which has been termed ocean acidification (OA). The impacts of pCO₂-driven acidification on immunity have been revealed recently in various marine organisms. However, the mechanism causing the reduction in phagocytosis still remains unclear. Therefore, the impacts of pCO₂-driven OA at present and near-future levels (pH values of 8.1, 7.8, and 7.4) on the rate of phagocytosis, the abundance of cytoskeleton components, the levels of nitric oxide (NO), and the concentration and activity of lysozymes (LZM) of hemocytes were investigated in a commercial bivalve species, the blood clam (Tegillarca granosa). In addition, the effects of OA on the expression of genes regulating actin skeleton and nitric oxide synthesis 2 (NOS2) were also analyzed. The results obtained showed that the phagocytic rate, cytoskeleton component abundance, concentration and activity of LZM of hemocytes were all significantly reduced after a 2-week exposure to the future OA scenario of a pH of 7.4. On the contrary, a remarkable increase in the concentration of NO compared to that of the control was detected in clams exposed to OA. Furthermore, the expression of genes regulating the actin cytoskeleton and NOS were significantly up-regulated after OA exposure. Though the mechanism causing phagocytosis seemed to be complicated based on the results obtained in the present study and those reported previously, our results suggested that OA may reduce the phagocytosis of hemocytes by (1) decreasing the abundance of cytoskeleton components and therefore hampering the cytoskeleton-mediated process of engulfment, (2) reducing the concentration and activity of LZM and therefore constraining the degradation of the engulfed pathogen through an oxygen-independent pathway, and (3) inducing the production of NO, which may negatively regulate immune responses.