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

Dual sgRNA-directed tyrosinases knockout using CRISPR/Cas9 technology in Pacific oyster (Crassostrea gigas) reveals their roles in early shell calcification

Biomineralization processes in bivalves, particularly the initial production of molecular components (such as matrix deposition and calcification) in the early stages of shell development are highly complex and well-organized. This study investigated the temporal dynamics of organic matrix and calcium carbonate (CaCO3) deposition in Pacific oysters (Crassostrea gigas) across various development stages. The shell-field initiated matrix secretion during the gastrula stage. Subsequent larval development triggered central shell-field calcification, accompanied by expansion of the calcium ring from its interior to the periphery. Notably, the expression patterns of CgTyrp-2 and CgTyr closely correlated with matrix deposition and calcification during early developmental stages, with peak expression occurring in oyster's gastrula and D-veliger stages. Subsequently, the CRISPR/Cas9 system was utilized to knock out CgTyrp-2 and CgTyr with more distinct phenotypic alterations observed when both genes were concurrently knocked out. The relative gene expression was analyzed post-knockout, indicating that the knockout of CgTyr or CgTyrp-2 led to reduced expression of CgChs1, along with increased expression of CgChit4. Furthermore, when dual-sgRNAs were employed to knockout CgTyrp-2, a large deletion (2 kb) within the CgTyrp-2 gene was identified. In summary, early shell formation in C. gigas is the result of a complex interplay of multiple molecular components with CgTyrp-2 and CgTyr playing key roles in regulating CaCO3 deposition.

Core genes of biomineralization and cis-regulatory long non-coding RNA regulate shell growth in bivalves

INTRODUCTION

Bivalve molluscs are abundant in marine and freshwater systems and contribute essential ecosystem services. They are characterized by an exuberant diversity of biomineralized shells and typically have two symmetric valves (a.k.a shells), but oysters (Ostreidae), some clams (Anomiidae and Chamidae) and scallops (Pectinida) have two asymmetrical valves. Predicting and modelling the likely consequences of ocean acidification on bivalve survival, biodiversity and aquaculture makes understanding shell biomineralization and its regulation a priority.

OBJECTIVES

This study aimed to a) exploit the atypical asymmetric shell growth of some bivalves and through comparative analysis of the genome and transcriptome pinpoint candidate biomineralization-related genes and regulatory long non-coding RNAs (LncRNAs) and b) demonstrate their roles in regulating shell biomineralization/growth.

METHODS

Meta-analysis of genomes, de novo generated mantle transcriptomes or transcriptomes and proteomes from public databases for six asymmetric to symmetric bivalve species was used to identify biomineralization-related genes. Bioinformatics filtering uncovered genes and regulatory modules characteristic of bivalves with asymmetric shells and identified candidate biomineralization-related genes and lncRNAs with a biased expression in asymmetric valves. A shell regrowth model in oyster and gene silencing experiments, were used to characterize candidate gene function.

RESULTS

Shell matrix genes with asymmetric expression in the mantle of the two valves were identified and unique cis-regulatory lncRNA modules characterized in Ostreidae. LncRNAs that regulate the expression of the tissue inhibitor of metalloproteinases gene family (TIMPDR) and of the shell matrix protein domain family (SMPDR) were identified. In vitro and in vivo silencing experiments revealed the candidate genes and lncRNA were associated with divergent shell growth rates and modified the microstructure of calcium carbonate (CaCO3) crystals.

CONCLUSION

LncRNAs are putative regulatory factors of the bivalve biomineralization toolbox. In the Ostreidae family of bivalves biomineralization-related genes are cis-regulated by lncRNA and modify the planar growth rate and spatial orientation of crystals in the shell.

Comparative transcriptome analysis reveals molecular damage associated with cryopreservation in Crassostrea angulata D-larvae rather than to cryoprotectant exposure

BACKGROUND

The Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process.

RESULTS

Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 611 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were "carbohydrate metabolic process", "integral component of membrane" and "chitin binding" for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the "neuroactive ligand receptor interaction", "endocytosis" and "spliceosome" as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage.

CONCLUSIONS

The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.

Consequences of domestication in eastern oyster: Insights from whole genomic analyses

Selective breeding for production traits has yielded relatively rapid successes with high-fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1-17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild - wild] < [wild - cultured] < [cultured - cultured]. A genome scan for parallel adaptation to the captive environment applied two methodologically distinct outlier tests to the wild versus selected strain contrast and identified a total of 1174 candidate SNPs. Contrasting wild versus selected strains revealed the early evolutionary consequences of domestication in terms of genomic differentiation, standing genetic diversity, effective population size, relatedness, runs of homozygosity profiles, and genome-wide linkage disequilibrium patterns. Random Forest was used to identify 37 outlier SNPs that had the greatest discriminatory power between bulked wild and selected oysters. The outlier SNPs were in genes enriched for cytoskeletal functions, hinting at possible traits under inadvertent selection during larval culture or pediveliger setting at high density. This study documents rapid genomic changes stemming from hatchery-based cultivation of eastern oysters, identifies candidate loci responding to domestication in parallel among independent aquaculture strains, and provides potentially useful genomic resources for monitoring interbreeding between farm and wild oysters.

Unraveling the interplay between environmental microplastics and salinity stress on Mytilus galloprovincialis larval development: A holistic exploration

The rise of plastic production has triggered a surge in plastic waste, overwhelming marine ecosystems with microplastics. The effects of climate change, notably changing salinity, have shaped the dynamics of coastal lagoons. Thus, understanding the combined impact of these phenomena on marine organisms becomes increasingly crucial. To address these knowledge gaps, we investigated for the first time the interactive effects of environmental microplastics (EMPs) and increased salinity on the early development of Mytilus galloprovincialis larvae. Morphological assessments using the larval embryotoxicity test revealed larval anomalies and developmental arrests induced by EMPs and increased salinity. Transcriptomic analyses targeting 12 genes involved in oxidative stress, apoptosis, DNA repair, shell formation, and stress proteins were conducted on D-larvae uncovered the potential effects of EMPs on shell biomineralization, highlighting the role of Histidine Rich Glycoproteine (HRG) and tubulin as crucial adaptive mechanisms in Mytilus sp. in response to environmental shifts. Furthermore, we explored oxidative stress and neurotoxicity using biochemical assays. Our findings revealed a potential interaction between EMPs and increased salinity, impacting multiple physiological processes in mussel larvae. Our data contribute to understanding the cumulative effects of emerging anthropogenic pollutants and environmental stressors, emphasizing the need for a holistic approach to assessing their impact on marine ecosystems.

Transcriptomic Responses of a Lightly Calcified Echinoderm to Experimental Seawater Acidification and Warming during Early Development

Ocean acidification (OA) and ocean warming (OW) are potential obstacles to the survival and growth of marine organisms, particularly those that rely on calcification. This study investigated the single and joint effects of OA and OW on sea cucumber Apostichopus japonicus larvae raised under combinations of two temperatures (19 °C or 22 °C) and two pCO2 levels (400 or 1000 μatm) that reflect the current and end-of-21st-century projected ocean scenarios. The investigation focused on assessing larval development and identifying differences in gene expression patterns at four crucial embryo-larval stages (blastula, gastrula, auricularia, and doliolaria) of sea cucumbers, using RNA-seq. Results showed the detrimental effect of OA on the early development and body growth of A. japonicus larvae and a reduction in the expression of genes associated with biomineralization, skeletogenesis, and ion homeostasis. This effect was particularly pronounced during the doliolaria stage, indicating the presence of bottlenecks in larval development at this transition phase between the larval and megalopa stages in response to OA. OW accelerated the larval development across four stages of A. japonicus, especially at the blastula and doliolaria stages, but resulted in a widespread upregulation of genes related to heat shock proteins, antioxidant defense, and immune response. Significantly, the negative effects of elevated pCO2 on the developmental process of larvae appeared to be mitigated when accompanied by increased temperatures at the expense of reduced immune resilience and increased system fragility. These findings suggest that alterations in gene expression within the larvae of A. japonicus provide a mechanism to adapt to stressors arising from a rapidly changing oceanic environment.

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.

RNAi Silencing of the Biomineralization Gene Perlucin Impairs Oyster Ability to Cope with Ocean Acidification

Calcifying marine organisms, including the eastern oyster (Crassostrea virginica), are vulnerable to ocean acidification (OA) because it is more difficult to precipitate calcium carbonate (CaCO₃). Previous investigations of the molecular mechanisms associated with resilience to OA in C. virginica demonstrated significant differences in single nucleotide polymorphism and gene expression profiles among oysters reared under ambient and OA conditions. Converged evidence generated by both of these approaches highlighted the role of genes related to biomineralization, including perlucins. Here, gene silencing via RNA interference (RNAi) was used to evaluate the protective role of a perlucin gene under OA stress. Larvae were exposed to short dicer-substrate small interfering RNA (DsiRNA-perlucin) to silence the target gene or to one of two control treatments (control DsiRNA or seawater) before cultivation under OA (pH ~7.3) or ambient (pH ~8.2) conditions. Two transfection experiments were performed in parallel, one during fertilization and one during early larval development (6 h post-fertilization), before larval viability, size, development, and shell mineralization were monitored. Silenced oysters under acidification stress were the smallest, had shell abnormalities, and had significantly reduced shell mineralization, thereby suggesting that perlucin significantly helps larvae mitigate the effects of OA.

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.

Directional fabrication and dissolution of larval and juvenile oyster shells under ocean acidification

Biomineralization is one of the key biochemical processes in calcifying bivalve species such as oysters that is affected by ocean acidification (OA). Larval life stages of oysters are made of aragonite crystals whereas the adults are made of calcite and/or aragonite. Though both calcite and aragonite are crystal polymorphs of calcium carbonate, they have different mechanical properties and hence it is important to study the micro and nano structure of different life stages of oyster shells under OA to understand the mechanisms by which OA affects biomineralization ontogeny. Here, we have studied the larval and juvenile life stages of an economically and ecologically important estuarine oyster species, Crassostrea hongkongensis, under OA with focus over shell fabrication under OA (pHNBS 7.4). We also look at the effect of parental exposure to OA on larvae and juvenile microstructure. The micro and nanostructure characterization reveals directional fabrication of oyster shells, with more organized structure as biomineralization progresses. Under OA, both the larval and juvenile stages show directional dissolution, i.e. the earlier formed shell layers undergo dissolution at first, owing to longer exposure time. Despite dissolution, the micro and nanostructure of the shell remains unaffected under OA, irrespective of parental exposure history.

Proteomic and Transcriptomic Responses Enable Clams to Correct the pH of Calcifying Fluids and Sustain Biomineralization in Acidified Environments

Seawater pH and carbonate saturation are predicted to decrease dramatically by the end of the century. This process, designated ocean acidification (OA), threatens economically and ecologically important marine calcifiers, including the northern quahog (Mercenaria mercenaria). While many studies have demonstrated the adverse impacts of OA on bivalves, much less is known about mechanisms of resilience and adaptive strategies. Here, we examined clam responses to OA by evaluating cellular (hemocyte activities) and molecular (high-throughput proteomics, RNASeq) changes in hemolymph and extrapallial fluid (EPF-the site of biomineralization located between the mantle and the shell) in M. mercenaria continuously exposed to acidified (pH ~7.3; pCO₂ ~2700 ppm) and normal conditions (pH ~8.1; pCO₂ ~600 ppm) for one year. The extracellular pH of EPF and hemolymph (~7.5) was significantly higher than that of the external acidified seawater (~7.3). Under OA conditions, granulocytes (a sub-population of hemocytes important for biomineralization) were able to increase intracellular pH (by 54% in EPF and 79% in hemolymph) and calcium content (by 56% in hemolymph). The increased pH of EPF and hemolymph from clams exposed to high pCO₂ was associated with the overexpression of genes (at both the mRNA and protein levels) related to biomineralization, acid-base balance, and calcium homeostasis, suggesting that clams can use corrective mechanisms to mitigate the negative impact of OA.

Convergent evolution of barnacles and molluscs sheds lights in origin and diversification of calcareous shell and sessile lifestyle

The calcareous shell and sessile lifestyle are the representative phenotypes of many molluscs, which happen to be present in barnacles, a group of unique crustaceans. The origin of these phenotypes is unclear, but it may be embodied in the convergent genetics of such distant groups (interphylum). Herein, we perform comprehensive comparative genomics analysis in barnacles and molluscs, and reveal a genome-wide strong convergent molecular evolution between them, including coexpansion of biomineralization and organic matrix genes for shell formation, and origination of lineage-specific orphan genes for settlement. Notably, the expanded biomineralization gene encoding alkaline phosphatase evolves a novel, highly conserved motif that may trigger the origin of barnacle shell formation. Unlike molluscs, barnacles adopt novel organic matrices and cement proteins for shell formation and settlement, respectively, and their calcareous shells have potentially originated from the cuticle system of crustaceans. Therefore, our study corroborates the idea that selection pressures driving convergent evolution may strongly act in organisms inhabiting similar environments regardless of phylogenetic distance. The convergence signatures shed light on the origin of the shell and sessile lifestyle of barnacles and molluscs. In addition, notable non-convergence signatures are also present and may contribute to morphological and functional specificities.

Identification and Characterization of the Larval Settlement Pheromone Protein Components in Adult Shells of Crassostrea gigas: A Novel Function of Shell Matrix Proteins

The global decline of natural oyster populations emphasizes the need to improve our understanding of their biology. Understanding the role of chemical cues from conspecifics on how oysters occupy appropriate substrata is crucial to learning about their evolution, population dynamics, and chemical communication. Here, a novel role of a macromolecular assembly of shell matrix proteins which act as Crassostrea gigas Settlement Pheromone Protein Components in adult shells is demonstrated as the biological cue responsible for gregarious settlement on conspecifics. A bioassay-guided fractionation approach aided by biochemical and molecular analyses reveals that Gigasin-6 isoform X1 and/or X2 isolated from adult shells is the major inducing cue for larval settlement and may also play a role in postlarva–larva settlement interactions. Other isolated Stains-all-stainable acidic proteins may function as a co-factor and a scaffold/structural framework for other matrix proteins to anchor within this assembly and provide protection. Notably, conspecific cue-mediated larval settlement induction in C. gigas presents a complex system that requires an interplay of different glycans, disulfide bonds, amino acid groups, and phosphorylation crosstalk for recognition. These results may find application in the development of oyster aquacultures which could help recover declining marine species and as targets of anti-fouling agents.

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.

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.

Transcriptome Dynamics of an Oyster Larval Response to a Conspecific Cue-Mediated Settlement Induction in the Pacific Oyster Crassostrea gigas

The molecular mechanisms underlying the conspecific cue-mediated larval settlement in Crassostrea gigas is not yet fully understood. In this study, we described and compared the transcriptomes of competent pediveligers (Pedi) and conspecific cue-induced postlarvae (PL). A total of 2383 candidate transcripts were identified: 740 upregulated and 1643 downregulated transcripts, after settlement. Gene Ontology analysis revealed active chitin binding, calcium ion binding, and extracellular region processes in both stages. Results showed that the differential expression trend of six candidate transcripts were consistent between the quantitative real-time PCR and transcriptome data. The differential transcript expression related to shell formation showed closely linked dynamics with a gene regulatory network that may involve the interplay of various hormone receptors, neurotransmitters, and neuropeptide receptors working together in a concerted way in the Pedi and PL stages. Our results highlight the transcriptome dynamics underlying the settlement of oysters on conspecific adult shells and demonstrate the potential use of this cue as an attractant for wild and hatchery-grown oyster larval attachment on artificial substrates. It also suggests the possible involvement of an ecdysone signal pathway that may be linked to a neuroendocrine-biomineralization crosstalk in C. gigas settlement.

Ocean Acidification Alters Developmental Timing and Gene Expression of Ion Transport Proteins During Larval Development in Resilient and Susceptible Lineages of the Pacific Oyster (Crassostrea gigas)

Ocean acidification (OA) adversely impacts initial shell formation of bivalve larvae. Despite many studies observing large differences in developmental success between distinct genetic populations of bivalves exposed to OA, few studies have investigated the molecular mechanisms that enable resilient larvae to build their initial shell in aragonite-undersaturated conditions. This knowledge is key to their ecological and economical conservation. Herein, we used a genetic-selection program for Crassostrea gigas to produce a resilient and susceptible larval lineage to OA. The resilient and susceptible larvae were sampled every 3 h over a 24-h period in aragonite-undersaturated and control conditions. The susceptible lineage failed to develop a larval shell in aragonite-undersaturated conditions, whereas 52% of the resilient lineage developed to D-larvae by 24 h post fertilisation. We measured the expression of 23 genes involved in initial shell formation by RT-qPCR, which revealed significant genotype-by-time and environment-by-time interactions for the transcription of these genes. Aragonite-undersaturated conditions upregulated a single gene encoding a protein involved in ion transport, Na⁺ K⁺ ATPase, in both the resilient and susceptible lineage. These results were corroborated by a second experiment involving 25 pair-mated C. gigas families exposed to aragonite-undersaturated and control conditions. Our findings indicate C. gigas have a fixed capacity to modulate expression of genes involved in initial shell formation in response to OA. Thus, phenotypic differences to OA between the resilient and susceptible lineage are likely explained by other cellular processes, such as bioenergetics or protein translation.

Single-Larva RNA Sequencing Identifies Markers of Copper Toxicity and Exposure in Early Mytilus californianus Larvae

One of the challenges facing efforts to generate molecular biomarkers for toxins is distinguishing between markers that are indicative of exposure and markers that provide evidence of the effects of toxicity. Phenotypic anchoring provides an approach to help segregate markers into these categories based on some phenotypic index of toxicity. Here we leveraged the mussel embryo-larval toxicity assay in which toxicity is estimated by the fraction of larvae that exhibit an abnormal morphology, to isolate subsets of larvae that were abnormal and thus showed evidence of copper-toxicity, versus others that while exposed to copper exhibited normal morphology. Mussel larvae reared under control conditions or in the presence of increasing levels of copper (3-15 μg/L Cu²⁺) were physically sorted according to whether their morphology was normal or abnormal, and then profiled using RNAseq. Supervised differential expression analysis identified sets of genes whose differential expression was specific to the pools of abnormal larvae versus normal larvae, providing putative markers of copper toxicity versus exposure. Markers of copper exposure and copper-induced abnormality were involved in many of the same pathways, including development, shell formation, cell adhesion, and oxidative stress, yet unique markers were detected in each gene set. Markers of effect appeared to be more resolving between phenotypes at the lower copper concentration, while markers of exposure were informative at both copper concentrations.

Draft genome of Semisulcospira libertina, a species of freshwater snail

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Although S. libertina has ecological, commercial, and clinical importance, its whole-genome has not been reported yet. Here, we revealed the genome of S. libertina through de novo assembly. We assembled the whole-genome of S. libertina and determined its transcriptome for the first time using Illumina NovaSeq 6000 platform. According to the k-mer analysis, the genome size of S. libertina was estimated to be 3.04 Gb. Using RepeatMasker, a total of 53.68% of repeats were identified in the genome assembly. Genome data of S. libertina reported in this study will be useful for identification and conservation of S. libertina in East Asia.

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.

Larval development in the Pacific oyster and the impacts of ocean acidification: Differential genetic effects in wild and domesticated stocks

The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO2 seawater for these species is a trait with a genetic basis and variability in natural populations. To date, however, it remains unclear how the selective effects of OA occur within the context of complex genetic interactions underpinning larval development in many of the most vulnerable taxa. Here we evaluated phenotypic and genetic changes during larval development of Pacific oysters (Crassostrea gigas) reared in ambient (~400 µatm) and high (~1600 µatm) pCO2 conditions, both in domesticated and naturalized "wild" oysters from the Pacific Northwest, USA. Using pooled DNA samples, we determined changes in allele frequencies across larval development, from early "D-stage" larvae to metamorphosed juveniles (spat), in both groups and environments. Domesticated larvae had ~26% fewer loci with changing allele frequencies across developmental stages and <50% as many loci affected by acidified culture conditions, compared to larvae from wild broodstock. Functional enrichment analyses of genetic markers with significant changes in allele frequency revealed that the structure and function of cellular membranes were disproportionately affected by high pCO2 conditions in both groups. These results indicate the potential for a rapid adaptive response of oyster populations to OA conditions; however, underlying genetic changes associated with larval development differ between these wild and domesticated oyster stocks and influence their adaptive responses to OA conditions.

Copper promoting oyster larval growth and settlement: Molecular insights from RNA-seq

As a cofactor of key enzymes, Cu is required in living organisms, although Cu levels in the natural environment are typically low. In this study, the promotion of growth and settlement on the larvae of oyster Crassostrea angulata was observed at an environmentally relevant concentration (10 μg/L Cu). Interestingly, Cu accumulation in the soft tissue of oyster larvae increased during the larval development and exhibited a sharp increase at the late pelagic stage. With the help of RNA-seq, we constructed a high-quality transcriptional database of the oyster C. angulata larvae (24,257 genes with an average length of 1594 bp) via de novo assembly, which provided the basic molecular changes during the larval development. Network analysis of five early developmental stages and differential expression under Cu exposure were integrated to examine the roles of Cu in oyster larvae. Our molecular analysis demonstrated that both ion channels and organic transporters contributed to Cu internalization from the external environment, including zinc transporters and amino acid transporters. The followed distribution of Cu across cells was achieved by ATP7A, the circulatory system, and the Cu transporters (CTRs). Cu exposure enhanced the ribosome and the calcium binding proteins with a higher rate of translation and shell formation, giving rise to faster growth of oyster larvae. Furthermore, Cu facilitated the settling process by upregulating the chitin binding genes and then promoting the formation of the proteinaceous matrix between larvae and substrate. Our study presents the molecular basis for Cu promotion (i.e., hormesis) effects on oyster larval growth and settlement.

Oyster biomineralization under ocean acidification: From genes to shell

Biomineralization is one of the key processes that is notably affected in marine calcifiers such as oysters under ocean acidification (OA). Understanding molecular changes in the biomineralization process under OA and its heritability, therefore, is key to developing conservation strategies for protecting ecologically and economically important oyster species. To do this, in this study, we have explicitly chosen the tissue involved in biomineralization (mantle) of an estuarine commercial oyster species, Crassostrea hongkongensis. The primary aim of this study is to understand the influence of DNA methylation over gene expression of mantle tissue under decreased ~pH 7.4, a proxy of OA, and to extrapolate if these molecular changes can be observed in the product of biomineralization-the shell. We grew early juvenile C. hongkongensis, under decreased ~pH 7.4 and control ~pH 8.0 over 4.5 months and studied OA-induced DNA methylation and gene expression patterns along with shell properties such as microstructure, crystal orientation and hardness. The population of oysters used in this study was found to be moderately resilient to OA at the end of the experiment. The expression of key biomineralization-related genes such as carbonic anhydrase and alkaline phosphatase remained unaffected; thus, the mechanical properties of the shell (shell growth rate, hardness and crystal orientation) were also maintained without any significant difference between control and OA conditions with signs of severe dissolution. In addition, this study makes three major conclusions: (1) higher expression of Ca²⁺ binding/signalling-related genes in the mantle plays a key role in maintaining biomineralization under OA; (2) DNA methylation changes occur in response to OA; however, these methylation changes do not directly control gene expression; and (3) OA would be more of a 'dissolution problem' rather than a 'biomineralization problem' for resilient species that maintain calcification rate with normal shell growth and mechanical properties.

Effects of acidified seawater on biological and physiological responses of Artemia franciscana

Ocean acidification is becoming a potential threat to marine animals. The present study investigated the effect of seawater acidification on Artemia franciscana. A. franciscana cysts were allowed to hatch at different pH levels of pH 8.2 (control), 7.8, and 6.8. After 48 h incubation, the hatching percentage was significantly reduced in acidified seawater compared to that in control. Further, the hatched Artemia nauplii from each pH treatment were transferred to freshly acidified seawater for chronic study for 15 days. At the end of the experiment, survival, growth, and biochemical constituents were significantly decreased in Artemia at pH 7.8 and 6.8 compared to that in control, which indicates the adverse effects of acidified seawater on Artemia. The antioxidants, lipid peroxidation, and metabolic enzymes were significantly elevated in A. franciscana exposed to acidified seawater compared to that in control, which shows oxidative and metabolic stress on A. franciscana under acidified environment.

Transcriptomic analysis of shell repair and biomineralization in the blue mussel, Mytilus edulis

BACKGROUND

Biomineralization by molluscs involves regulated deposition of calcium carbonate crystals within a protein framework to produce complex biocomposite structures. Effective biomineralization is a key trait for aquaculture, and animal resilience under future climate change. While many enzymes and structural proteins have been identified from the shell and in mantle tissue, understanding biomieralization is impeded by a lack of fundamental knowledge of the genes and pathways involved. In adult bivalves, shells are secreted by the mantle tissue during growth, maintenance and repair, with the repair process, in particular, amenable to experimental dissection at the transcriptomic level in individual animals.

RESULTS

Gene expression dynamics were explored in the adult blue mussel, Mytilus edulis, during experimentally induced shell repair, using the two valves of each animal as a matched treatment-control pair. Gene expression was assessed using high-resolution RNA-Seq against a de novo assembled database of functionally annotated transcripts. A large number of differentially expressed transcripts were identified in the repair process. Analysis focused on genes encoding proteins and domains identified in shell biology, using a new database of proteins and domains previously implicated in biomineralization in mussels and other molluscs. The genes implicated in repair included many otherwise novel transcripts that encoded proteins with domains found in other shell matrix proteins, as well as genes previously associated with primary shell formation in larvae. Genes with roles in intracellular signalling and maintenance of membrane resting potential were among the loci implicated in the repair process. While haemocytes have been proposed to be actively involved in repair, no evidence was found for this in the M. edulis data.

CONCLUSIONS

The shell repair experimental model and a newly developed shell protein domain database efficiently identified transcripts involved in M. edulis shell production. In particular, the matched pair analysis allowed factoring out of much of the inherent high level of variability between individual mussels. This snapshot of the damage repair process identified a large number of genes putatively involved in biomineralization from initial signalling, through calcium mobilization to shell construction, providing many novel transcripts for future in-depth functional analyses.

Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma

Ocean acidification (OA) from seawater uptake of rising carbon dioxide emissions impairs development in marine invertebrates, particularly in calcifying species. Plasticity in gene expression is thought to mediate many of these physiological effects, but how these responses change across life history stages remains unclear. The abbreviated lecithotrophic development of the sea urchin Heliocidaris erythrogramma provides a valuable opportunity to analyse gene expression responses across a wide range of life history stages, including the benthic, post-metamorphic juvenile. We measured the transcriptional response to OA in H. erythrogramma at three stages of the life cycle (embryo, larva, and juvenile) in a controlled breeding design. The results reveal a broad range of strikingly stage-specific impacts of OA on transcription, including changes in the number and identity of affected genes; the magnitude, sign, and variance of their expression response; and the developmental trajectory of expression. The impact of OA on transcription was notably modest in relation to gene expression changes during unperturbed development and much smaller than genetic contributions from parentage. The latter result suggests that natural populations may provide an extensive genetic reservoir of resilience to OA. Taken together, these results highlight the complexity of the molecular response to OA, its substantial life history stage specificity, and the importance of contextualizing the transcriptional response to pH stress in light of normal development and standing genetic variation to better understand the capacity for marine invertebrates to adapt to OA.

Intracellular pH regulation in mantle epithelial cells of the Pacific oyster, Crassostrea gigas

Shell formation and repair occurs under the control of mantle epithelial cells in bivalve molluscs. However, limited information is available on the precise acid–base regulatory machinery present within these cells, which are fundamental to calcification. Here, we isolate mantle epithelial cells from the Pacific oyster, Crassostrea gigas and utilise live cell imaging in combination with the fluorescent dye, BCECF-AM to study intracellular pH (pH_i) regulation. To elucidate the involvement of various ion transport mechanisms, modified seawater solutions (low sodium, low bicarbonate) and specific inhibitors for acid–base proteins were used. Diminished pH recovery in the absence of Na⁺ and under inhibition of sodium/hydrogen exchangers (NHEs) implicate the involvement of a sodium dependent cellular proton extrusion mechanism. In addition, pH recovery was reduced under inhibition of carbonic anhydrases. These data provide the foundation for a better understanding of acid–base regulation underlying the physiology of calcification in bivalves.

Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics

Most molluscs possess shells, constructed from a vast array of microstructures and architectures. The fully formed shell is composed of calcite or aragonite. These CaCO₃ crystals form complex biocomposites with proteins, which although typically less than 5% of total shell mass, play significant roles in determining shell microstructure. Despite much research effort, large knowledge gaps remain in how molluscs construct and maintain their shells, and how they produce such a great diversity of forms. Here we synthesize results on how shell shape, microstructure, composition and organic content vary among, and within, species in response to numerous biotic and abiotic factors. At the local level, temperature, food supply and predation cues significantly affect shell morphology, whilst salinity has a much stronger influence across latitudes. Moreover, we emphasize how advances in genomic technologies [e.g. restriction site-associated DNA sequencing (RAD-Seq) and epigenetics] allow detailed examinations of whether morphological changes result from phenotypic plasticity or genetic adaptation, or a combination of these. RAD-Seq has already identified single nucleotide polymorphisms associated with temperature and aquaculture practices, whilst epigenetic processes have been shown significantly to modify shell construction to local conditions in, for example, Antarctica and New Zealand. We also synthesize results on the costs of shell construction and explore how these affect energetic trade-offs in animal metabolism. The cellular costs are still debated, with CaCO₃ precipitation estimates ranging from 1-2 J/mg to 17-55 J/mg depending on experimental and environmental conditions. However, organic components are more expensive (~29 J/mg) and recent data indicate transmembrane calcium ion transporters can involve considerable costs. This review emphasizes the role that molecular analyses have played in demonstrating multiple evolutionary origins of biomineralization genes. Although these are characterized by lineage-specific proteins and unique combinations of co-opted genes, a small set of protein domains have been identified as a conserved biomineralization tool box. We further highlight the use of sequence data sets in providing candidate genes for in situ localization and protein function studies. The former has elucidated gene expression modularity in mantle tissue, improving understanding of the diversity of shell morphology synthesis. RNA interference (RNAi) and clustered regularly interspersed short palindromic repeats - CRISPR-associated protein 9 (CRISPR-Cas9) experiments have provided proof of concept for use in the functional investigation of mollusc gene sequences, showing for example that Pif (aragonite-binding) protein plays a significant role in structured nacre crystal growth and that the Lsdia1 gene sets shell chirality in Lymnaea stagnalis. Much research has focused on the impacts of ocean acidification on molluscs. Initial studies were predominantly pessimistic for future molluscan biodiversity. However, more sophisticated experiments incorporating selective breeding and multiple generations are identifying subtle effects and that variability within mollusc genomes has potential for adaption to future conditions. Furthermore, we highlight recent historical studies based on museum collections that demonstrate a greater resilience of molluscs to climate change compared with experimental data. The future of mollusc research lies not solely with ecological investigations into biodiversity, and this review synthesizes knowledge across disciplines to understand biomineralization. It spans research ranging from evolution and development, through predictions of biodiversity prospects and future-proofing of aquaculture to identifying new biomimetic opportunities and societal benefits from recycling shell products.

Molecular mechanisms of biomineralization in marine invertebrates

Much recent marine research has been directed towards understanding the effects of anthropogenic-induced environmental change on marine biodiversity, particularly for those animals with heavily calcified exoskeletons, such as corals, molluscs and urchins. This is because life in our oceans is becoming more challenging for these animals with changes in temperature, pH and salinity. In the future, it will be more energetically expensive to make marine skeletons and the increasingly corrosive conditions in seawater are expected to result in the dissolution of these external skeletons. However, initial predictions of wide-scale sensitivity are changing as we understand more about the mechanisms underpinning skeletal production (biomineralization). These studies demonstrate the complexity of calcification pathways and the cellular responses of animals to these altered conditions. Factors including parental conditioning, phenotypic plasticity and epigenetics can significantly impact the production of skeletons and thus future population success. This understanding is paralleled by an increase in our knowledge of the genes and proteins involved in biomineralization, particularly in some phyla, such as urchins, molluscs and corals. This Review will provide a broad overview of our current understanding of the factors affecting skeletal production in marine invertebrates. It will focus on the molecular mechanisms underpinning biomineralization and how knowledge of these processes affects experimental design and our ability to predict responses to climate change. Understanding marine biomineralization has many tangible benefits in our changing world, including improvements in conservation and aquaculture and exploitation of natural calcified structure design using biomimicry approaches that are aimed at producing novel biocomposites.

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.

Expression of calcification-related ion transporters during blue mussel larval development

The physiological processes driving the rapid rates of calcification in larval bivalves are poorly understood. Here, we use a calcification substrate-limited approach (low dissolved inorganic carbon, C T) and mRNA sequencing to identify proteins involved in bicarbonate acquisition during shell formation. As a secondary approach, we examined expression of ion transport and shell matrix proteins (SMPs) over the course of larval development and shell formation. We reared four families of Mytilus edulis under ambient (ca. 1865 µmol/kg) and low C T (ca. 941 µmol/kg) conditions and compared expression patterns at six developmental time points. Larvae reared under low C T exhibited a developmental delay, and a small subset of contigs was differentially regulated between ambient and low C T conditions. Of particular note was the identification of one contig encoding an anion transporter (SLC26) which was strongly upregulated (2.3-2.9 fold) under low C T conditions. By analyzing gene expression profiles over the course of larval development, we are able to isolate sequences encoding ion transport and SMPs to enhance our understanding of cellular pathways underlying larval calcification processes. In particular, we observe the differential expression of contigs encoding SLC4 family members (sodium bicarbonate cotransporters, anion exchangers), calcium-transporting ATPases, sodium/calcium exchangers, and SMPs such as nacrein, tyrosinase, and transcripts related to chitin production. With a range of candidate genes, this work identifies ion transport pathways in bivalve larvae and by applying comparative genomics to investigate temporal expression patterns, provides a foundation for further studies to functionally characterize the proteins involved in larval calcification.

The harmful algae, Cochlodinium polykrikoides and Aureococcus anophagefferens, elicit stronger transcriptomic and mortality response in larval bivalves (Argopecten irradians) than climate change stressors

Global ocean change threatens marine life, yet a mechanistic understanding of how organisms are affected by specific stressors is poorly understood. Here, we identify and compare the unique and common transcriptomic responses of an organism experiencing widespread fisheries declines, Argopecten irradians (bay scallop) exposed to multiple stressors including high pCO2, elevated temperature, and two species of harmful algae, Cochlodinium (aka Margalefidinium) polykrikoides and Aureococcus anophagefferens using high-throughput sequencing (RNA-seq). After 48 hr of exposure, scallop transcriptomes revealed distinct expression profiles with larvae exposed to harmful algae (C. polykrikoides and A. anophagefferens) displaying broader responses in terms of significantly and differentially expressed (DE) transcripts (44,922 and 4,973; respectively) than larvae exposed to low pH or elevated temperature (559 and 467; respectively). Patterns of expression between larvae exposed to each harmful algal treatment were, however, strikingly different with larvae exposed to A. anophagefferens displaying large, significant declines in the expression of transcripts (n = 3,615; 87% of DE transcripts) whereas exposure to C. polykrikoides increased the abundance of transcripts, more than all other treatments combined (n = 43,668; 97% of DE transcripts). Larvae exposed to each stressor up-regulated a common set of 21 genes associated with protein synthesis, cellular metabolism, shell growth, and membrane transport. Larvae exposed to C. polykrikoides displayed large increases in antioxidant-associated transcripts, whereas acidification-exposed larvae increased abundance of transcripts associated with shell formation. After 10 days of exposure, each harmful algae caused declines in survival that were significantly greater than all other treatments. Collectively, this study reveals the common and unique transcriptional responses of bivalve larvae to stressors that promote population declines within coastal zones, providing insight into the means by which they promote mortality as well as traits possessed by bay scallops that enable potential resistance.

From the raw bar to the bench: Bivalves as models for human health

Bivalves, from raw oysters to steamed clams, are popular choices among seafood lovers and once limited to the coastal areas. The rapid growth of the aquaculture industry and improvement in the preservation and transport of seafood have enabled them to be readily available anywhere in the world. Over the years, oysters, mussels, scallops, and clams have been the focus of research for improving the production, managing resources, and investigating basic biological and ecological questions. During this decade, an impressive amount of information using high-throughput genomic, transcriptomic and proteomic technologies has been produced in various classes of the Mollusca group, and it is anticipated that basic and applied research will significantly benefit from this resource. One aspect that is also taking momentum is the use of bivalves as a model system for human health. In this review, we highlight some of the aspects of the biology of bivalves that have direct implications in human health including the shell formation, stem cells and cell differentiation, the ability to fight opportunistic and specific pathogens in the absence of adaptive immunity, as source of alternative drugs, mucosal immunity and, microbiome turnover, toxicology, and cancer research. There is still a long way to go; however, the next time you order a dozen oysters at your favorite raw bar, think about a tasty model organism that will not only please your palate but also help unlock multiple aspects of molluscan biology and improve human health.

D1 dopamine receptor is involved in shell formation in larvae of Pacific oyster Crassostrea gigas

Dopamine (DA), a significant member of catecholamines, is reported to induce biomineralization of calcium carbonate vaterite microspheres via dopamine receptor (DR) in bivalves, implying the modulation of dopaminergic system on shell formation during larval development. In this research, a homologue of D1 type DR (CgD1DR-1) was identified from oyster Crassostrea gigas, whose full length cDNA was 1197 bp. It was widely expressed in various tissues of C. gigas, with the significantly higher levels in hepatopancreas, mantle, muscle and gill. During developmental stages, the mRNA transcripts of CgD1DR-1 in D-shape larvae were obviously higher (p < 0.05) than those in trochophore and umbo larvae, and CO₂ exposure could inhibit the synthesis of DA and mRNA expression of CgD1DR-1. After cell transfection and DA treatment, intracellular cAMP in cells with the expression of CgD1DR-1 increased significantly (p < 0.05). Furthermore, the incubation with SCH 23390 for the blockage of CgD1DR-1 significantly restrained the expressions of six shell formation-related genes including CgTyrosinase-1, CgTyrosinase-3, CgChitinaseLP, CgAMC, CgBMP and CgBMPR in trochophore and D-shape larvae. These results jointly suggested that DA together with its receptor CgD1DR-1 might be involved in shell formation during oyster larval development from trochophore to D-shape larvae, and CO₂-induced ocean acidification (OA) might influence marine bivalves by inhibiting the DA-D1DR pathway to prohibit their shell formation.