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

Effects of typhoon events on coastal hydrology, nutrients, and algal bloom dynamics: Insights from continuous observation and machine learning in semi-enclosed Zhanjiang Bay, China

Typhoons can induce variations in hydrodynamic conditions and biogeochemical processes, potentially escalating the risk of algal bloom occurrences impacting coastal ecosystems. However, the impacts of typhoons on instantaneous changes and the mechanisms behind typhoon-induced algal blooms remain poorly understood. This study utilized high-frequency in situ observation and machine learning model to track the dynamic variations in meteorological, hydrological, physicochemical, and Chlorophyll-a (Chl-a) levels through the complete Typhoon Talim landing in Zhanjiang Bay (ZJB) in July 2023. The results showed that a delayed onset of algal bloom occurring 10 days after typhoon's arrival. Subsequently, as temperatures reached a suitable range, with an ample supply of nutrients and water stability, Chl-a peaked at 121.49 μg L-1 in algal bloom period. Additionally, water temperature and air temperature decreased by 1.61 °C and 2.8 °C during the typhoon, respectively. In addition, wind speed and flow speed increased by 1.34 and 0.015 m s-1 h-1 to peak values, respectively. Moreover, the slow decline of 8.2 % in salinity suggested a substantial freshwater input, leading to an increase in nutrients. For instance, the mean DIN and DIP were 2.2 and 8.5 times higher than those of the pre-typhoon period, resulting in a decrease in DIN/DIP (closer to16) and the alleviation of P limitation. Furthermore, pH and dissolved oxygen (DO) were both low during the typhoon period and then peaked at 8.93 and 19.05 mg L-1 during the algal bloom period, respectively, but subsequently decreased, remaining lower than those of the pre-typhoon period. A preliminary learning machine model was established to predict Chl-a and exhibited good accuracy, with R2 of 0.73. This study revealed the mechanisms of eutrophication status formation and algal blooms occurrence in the coastal waters, providing insights into the effects of typhoon events on tropical coastal biogeochemistry and ecology.

Oyster reefs' control of carbonate chemistry-Implications for oyster reef restoration in estuaries subject to coastal ocean acidification

Globally, oyster reef restoration is one of the most widely applied coastal restoration interventions. While reefs are focal points of processes tightly linked to the carbonate system such as shell formation and respiration, how these processes alter reef carbonate chemistry relative to the surrounding seawater is unclear. Moreover, coastal systems are increasingly impacted by coastal acidification, which may affect reef carbonate chemistry. Here, we characterized the growth of multiple constructed reefs as well as summer variations in pH and carbonate chemistry of reef-influenced seawater (in the middle of reefs) and ambient seawater (at locations ~50 m outside of reefs) to determine how reef chemistry was altered by the reef community and, in turn, impacts resident oysters. High frequency monitoring across three subtidal constructed reefs revealed reductions of daily mean and minimum pH (by 0.05-0.07 and 0.07-0.12 units, respectively) in seawater overlying reefs relative to ambient seawater (p < .0001). The proportion of pH measurements below 7.5, a threshold shown to negatively impact post-larval oysters, were 1.8×-5.2× higher in reef seawater relative to ambient seawater. Most reef seawater samples (83%) were reduced in total alkalinity relative to ambient seawater samples, suggesting community calcification was a key driver of modified carbonate chemistry. The net metabolic influence of the reef community resulted in reductions of CaCO3 saturation state in 78% of discrete samples, and juvenile oysters placed on reefs exhibited slower shell growth (p < .05) compared to oysters placed outside of reefs. While differences in survival were not detected, reef oysters may benefit from enhanced survival or recruitment at the cost of slowed growth rates. Nevertheless, subtidal restored reef communities modified seawater carbonate chemistry in ways that likely increased oyster vulnerability to acidification, suggesting that carbonate chemistry dynamics warrant consideration when determining site suitability for oyster restoration, particularly under continued climate change.

Direct, carryover, and maternal effects of ocean acidification on snow crab embryos and larvae

Ocean acidification, a decrease in ocean pH with increasing anthropogenic CO2 concentrations, is expected to affect many marine animals. To examine the effects of decreased pH on snow crab (Chionoecetes opilio), a commercial species in Alaska, we reared ovigerous females in one of three treatments: Ambient pH (~8.1), pH 7.8, and pH 7.5, through two annual reproductive cycles. Morphometric changes during development and hatching success were measured for embryos both years and calcification was measured for the adult females at the end of the 2-year experiment. Embryos and larvae analyzed in year one were from oocytes developed, fertilized, and extruded in situ, whereas embryos and larvae in year two were from oocytes developed, fertilized, and extruded under acidified conditions in the laboratory. In both years, larvae were exposed to the same pH treatments in a fully crossed experimental design. Starvation-survival, morphology, condition, and calcium/magnesium content were assessed for larvae. Embryo morphology during development, hatching success, and fecundity were unaffected by pH during both years. Percent calcium in adult females' carapaces did not differ among treatments at the end of the experiment. In the first year, starvation-survival of larvae reared at Ambient pH but hatched from embryos reared at reduced pH was lowered; however, the negative effect was eliminated when the larvae were reared at reduced pH. In the second year, there was no direct effect of either embryo or larval pH treatment, but larvae reared as embryos at reduced pH survived longer if reared at reduced pH. Treatment either did not affect other measured larval parameters, or effect sizes were small. The results from this two-year study suggest that snow crabs are well adapted to projected ocean pH levels within the next two centuries, although other life-history stages still need to be examined for sensitivity and potential interactive effects with increasing temperatures should be investigated.

Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters

BACKGROUND

Molluscan shell, composed of a diverse range of architectures and microstructures, is a classic model system to study the relationships between molecular evolution and biomineralized structure formation. The shells of oysters differ from those of other molluscs by possessing a novel microstructure, chalky calcite, which facilitates adaptation to the sessile lifestyle. However, the genetic basis and evolutionary origin of this adaptive innovation remain largely unexplored.

RESULTS

We report the first whole-genome assembly and shell proteomes of the Iwagaki oyster Crassostrea nippona. Multi-omic integrative analyses revealed that independently expanded and co-opted tyrosinase, peroxidase, TIMP genes may contribute to the chalky layer formation in oysters. Comparisons with other molluscan shell proteomes imply that von Willebrand factor type A and chitin-binding domains are basic members of molluscan biomineralization toolkit. Genome-wide identification and analyses of these two domains in 19 metazoans enabled us to propose that the well-known Pif may share a common origin in the last common ancestor of Bilateria. Furthermore, Pif and LamG3 genes acquire new genetic function for shell mineralization in bivalves and the chalky calcite formation in oysters likely through a combination of gene duplication and domain reorganization.

CONCLUSIONS

The spatial expression of SMP genes in the mantle and molecular evolution of Pif are potentially involved in regulation of the chalky calcite deposition, thereby shaping the high plasticity of the oyster shell to adapt to a sessile lifestyle. This study further highlights neo-functionalization as a crucial mechanism for the diversification of shell mineralization and microstructures in molluscs, which may be applied more widely for studies on the evolution of metazoan biomineralization.

The involvement of a novel calmodulin-like protein isoform from oyster Crassostrea gigas in transcription factor regulation provides new insight into acclimation to ocean acidification

Marine organisms need to adapt to improve organismal fitness under ocean acidification (OA). Recent studies have shown that marine calcifiers can achieve acclimation by stimulating calcium binding/signaling pathways. Here, a CaM-like gene (CgCaLP-2) from oyster Crassostrea gigas which typically responded to long-term CO₂ exposure (two months) rather than short-term exposure (one week) was characterized. The cloned cDNA was 678 bp and was shorter than the retrieved sequence from NCBI (1125 bp). The two sequences, designated as CgCaLP-2-v1 and CgCaLP-2-v2, were demonstrated to be different splice variants by the genome sequence analysis. Western blotting analysis revealed two bands of 23 kD and 43 kD in mantle and hemocytes, corresponding to predicted molecular weight of CgCaLP-2-v1 and CgCaLP-2-v2, respectively. The isoform CgCaLP-2-v1 (the 23 kD band) was highly stimulated in response to long-term CO₂ exposure (42-day and 56-day treatment) in hemocytes and mantle tissue. The fluorescence signal of CgCaLP-2 in mantle and hemocytes became more intensive after long-term CO₂ exposure. Besides, in hemocytes, CgCaLP-2 presented a higher localization on the nuclear membrane after long-term CO₂ exposure (56 d). The target gene network of CgCaLP-2 was predicted, and a transcription factor (TF) gene annotated as Homeobox protein SIX4 (CgSIX4) showed a similar expressive trend to CgCaLP-2 during CO₂ exposure. Suppression of CgCaLP-2 via RNA interference significantly reduced the mRNA expression of CgSIX4. The results suggested that CgCaLP-2 might mediate the Ca²⁺-CaLP-TF signal transduction pathway under long-term CO₂ exposure. This study serves as an example to reveal that alternative splicing is an important mechanism for generation multiple protein isoforms and thus shape the plastic responses under CO₂ exposure, providing new insight into the potential acclimation ability of marine calcifiers to future OA.

Ocean acidification, warming and feeding impacts on biomineralization pathways and shell material properties of Magallana gigas and Mytilus spp

Molluscs are among the organisms affected by ocean acidification (OA), relying on carbon for shell biomineralization. Metabolic and environmental sourcing are two pathways potentially affected by OA, but the circumstances and patterns by which they are altered are poorly understood. From previous studies, mollusc shells grown under OA appear smaller in size, brittle and thinner, suggesting an important alteration in carbon sequestration. However, supplementary feeding experiments have shown promising results in offsetting the negative consequences of OA on shell growth. Our study compared carbon uptake by δ¹³C tracing and deposition into mantle tissue and shell layers in Magallana gigas and Mytilus species, two economically valuable and common species. After subjecting the species to 7.7 pH, +2 °C seawater, and enhanced feeding, both species maintain shell growth and metabolic pathways under OA without benefitting from extra feeding, thus, showing effective acclimation to rapid and short-term environmental change. Mytilus spp. increases metabolic carbon into the calcite and environmental sourcing of carbon into the shell aragonite in low pH and high temperature conditions. Low pH affects M. gigas mantle nitrogen isotopes maintaining growth. Calcite biomineralization pathway differs between the two species and suggests species-specific response 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.

Molecular basis of ocean acidification sensitivity and adaptation in Mytilus galloprovincialis

Predicting the potential for species adaption to climate change is challenged by the need to identify the physiological mechanisms that underpin species vulnerability. Here, we investigated the sensitivity to ocean acidification in marine mussels during early development, and specifically the trochophore stage. Using RNA and DNA sequencing and in situ RNA hybridization, we identified developmental processes associated with abnormal development and rapid adaptation to low pH. Trochophores exposed to low pH seawater exhibited 43 differentially expressed genes. Gene annotation and in situ hybridization of differentially expressed genes point to pH sensitivity of (1) shell field development and (2) cellular stress response. Five genes within these two processes exhibited shifts in allele frequencies indicative of a potential for rapid adaptation. This case study contributes direct evidence that protecting species’ existing genetic diversity is a critical management action to facilitate species resilience to climate change.

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Marine mussel larval development and genetic adaptation in low pH seawater

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RNA and DNA responses reveal impacts on shell field development and cell stress

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Five genes exhibited both physiological sensitivity and long-term adaptive potential

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Conserving standing genetic variation could bolster resilience to global change

A calcification-related calmodulin-like protein in the oyster Crassostrea gigas mediates the enhanced calcium deposition induced by CO2 exposure

Calcium transportation and homeostasis are essential for marine bivalves to maintain basic metabolism and build their shells. Calmodulin-like proteins (CaLPs) are important calcium sensors and buffers and can respond to ocean acidification (OA) in marine calcifiers. However, no further study of their physiological function in calcium metabolism under elevated CO₂ has been performed. Here, we identified a novel CaLP (designated CgCaLP) in the Pacific oyster Crassostrea gigas and demonstrated its participation in the calcification process: the mRNA expression level of CgCaLP peaked at the trochophore larval stage and remained high at stages when shells were shaped; the mRNA and protein of CgCaLP were more highly expressed in mantle tissue than in other tissues. Under elevated CO₂ levels, the protein expression level of CgCaLP in hemocytes increased, while in contrast, significantly decreased protein levels were detected in gill and mantle tissues. Shell dissolution caused the imbalance of calcium in hemocytes and decreased calcium absorption and transportation demand in gill and mantle tissues, inducing the molecular function allocation of CgCaLP under CO₂ exposure. Despite the decreased protein level in mantle tissue, CgCaLP was found to translocate to outer mantle epithelium (OME) cells where condensed calcium-rich deposits (CRDs) were detected. We further demonstrated that CgCaLP mRNA and protein expression levels could respond to seawater Ca²⁺ availability, suggesting that the calcium deposition capacity of oysters might be enhanced to fight against shell dissolution problems and that CgCaLP might serve as an essential participator of the process. In summary, CgCaLP might enhance calcium deposition under CO₂ exposure and thus play a significant and flexible molecular function involved in a compensation strategy of oysters to fight against the acidified ocean.

Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis)

The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed across Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to overexploitation and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was in the low-moderate range, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels was assessed. Genomic prediction accuracies using the full density panel were high (> 0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e., 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relatedness should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

Selection Experiments in the Sea: What Can Experimental Evolution Tell Us About How Marine Life Will Respond to Climate Change?

AbstractRapid evolution may provide a buffer against extinction risk for some species threatened by climate change; however, the capacity to evolve rapidly enough to keep pace with changing environments is unknown for most taxa. The ecosystem-level consequences of climate adaptation are likely to be the largest in marine ecosystems, where short-lived phytoplankton with large effective population sizes make up the bulk of primary production. However, there are substantial challenges to predicting climate-driven evolution in marine systems, including multiple simultaneous axes of change and considerable heterogeneity in rates of change, as well as the biphasic life cycles of many marine metazoans, which expose different life stages to disparate sources of selection. A critical tool for addressing these challenges is experimental evolution, where populations of organisms are directly exposed to controlled sources of selection to test evolutionary responses. We review the use of experimental evolution to test the capacity to adapt to climate change stressors in marine species. The application of experimental evolution in this context has grown dramatically in the past decade, shedding light on the capacity for evolution, associated trade-offs, and the genetic architecture of stress-tolerance traits. Our goal is to highlight the utility of this approach for investigating potential responses to climate change and point a way forward for future studies.

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.

Parental whole life cycle exposure modulates progeny responses to ocean acidification in slipper limpets

Multigenerational exposure is needed to assess the evolutionary potential of organisms in the rapidly changing seascape. Here, we investigate if there is a transgenerational effect of ocean acidification exposure on a calyptraeid gastropod such that long-term exposure elevates offspring resilience. Larvae from wild type Crepidula onyx adults were reared from hatching until sexual maturity for over 36 months under three pH conditions (pH 7.3, 7.7, and 8.0). While the survivorship, growth, and respiration rate of F₁ larvae were unaffected by acute ocean acidification (OA), long-term and whole life cycle exposure significantly compromised adult survivorship, growth, and reproductive output of the slipper limpets. When kept under low pH throughout their life cycle, only 6% of the F₁ slipper limpets survived pH 7.3 conditions after ~2.5 years and the number of larvae they released was ~10% of those released by the control. However, the F₂ progeny from adults kept under the long-term low pH condition hatched at a comparable size to those in medium and control pH conditions. More importantly, these F₂ progeny from low pH adults outperformed F₂ slipper limpets from control conditions; they had higher larval survivorship and growth, and reduced respiration rate across pH conditions, even at the extreme low pH of 7.0. The intragenerational negative consequences of OA during long-term acclimation highlights potential carryover effects and ontogenetic shifts in stress vulnerability, especially prior to and during reproduction. Yet, the presence of a transgenerational effect implies that this slipper limpet, which has been widely introduced along the West Pacific coasts, has the potential to adapt to rapid acidification.

Evolved differences in energy metabolism and growth dictate the impacts of ocean acidification on abalone aquaculture

The pH of the global ocean is decreasing due to the absorption of anthropogenically emitted CO₂, causing ocean acidification (OA). OA negatively impacts marine shellfish and threatens the continuing economic viability of molluscan shellfish aquaculture, a global industry valued at more than 19 billion USD. We identify traits linked to growth and lipid regulation that contribute tolerance to OA in abalone aquaculture, with broader implications for adaptation efforts in other shellfish species. We also identify evolved heritable variation for physiological resilience to OA that may be exploited in commercial and restoration aquaculture breeding programs to offset the negative consequences of continuing climate change.

Ocean acidification (OA) poses a major threat to marine ecosystems and shellfish aquaculture. A promising mitigation strategy is the identification and breeding of shellfish varieties exhibiting resilience to acidification stress. We experimentally compared the effects of OA on two populations of red abalone (Haliotis rufescens), a marine mollusc important to fisheries and global aquaculture. Results from our experiments simulating captive aquaculture conditions demonstrated that abalone sourced from a strong upwelling region were tolerant of ongoing OA, whereas a captive-raised population sourced from a region of weaker upwelling exhibited significant mortality and vulnerability to OA. This difference was linked to population-specific variation in the maternal provisioning of lipids to offspring, with a positive correlation between lipid concentrations and survival under OA. This relationship also persisted in experiments on second-generation animals, and larval lipid consumption rates varied among paternal crosses, which is consistent with the presence of genetic variation for physiological traits relevant for OA survival. Across experimental trials, growth rates differed among family lineages, and the highest mortality under OA occurred in the fastest growing crosses. Identifying traits that convey resilience to OA is critical to the continued success of abalone and other shellfish production, and these mitigation efforts should be incorporated into breeding programs for commercial and restoration aquaculture.

The impact of environmental acidification on the microstructure and mechanical integrity of marine invertebrate skeletons

Ocean acidification (OA), from seawater uptake of anthropogenic CO_2, has a suite of negative effects on the ability of marine invertebrates to produce and maintain their skeletons. Increased organism pCO₂ causes hypercapnia, an energetically costly physiological stress. OA alters seawater carbonate chemistry, limiting the carbonate available to form the calcium carbonate (CaCO₃) minerals used to build skeletons. The reduced saturation state of CaCO₃ also causes corrosion of CaCO₃ structures. Global change is also accelerating coastal acidification driven by land-run off (e.g. acid soil leachates, tannic acid). Building and maintaining marine biomaterials in the face of changing climate will depend on the balance between calcification and dissolution. Overall, in response to environmental acidification, many calcifiers produce less biomineral and so have smaller body size. Studies of skeleton development in echinoderms and molluscs across life stages show the stunting effect of OA. For corals, linear extension may be maintained, but at the expense of less dense biomineral. Conventional metrics used to quantify growth and calcification need to be augmented by characterisation of the changes to biomineral structure and mechanical integrity caused by environmental acidification. Scanning electron microscopy and microcomputed tomography of corals, tube worms and sea urchins exposed to experimental (laboratory) and natural (vents, coastal run off) acidification show a less dense biomineral with greater porosity and a larger void space. For bivalves, CaCO₃ crystal deposition is more chaotic in response to both ocean and coastal acidification. Biomechanics tests reveal that these changes result in weaker, more fragile skeletons, compromising their vital protective roles. Vulnerabilities differ among taxa and depend on acidification level. Climate warming has the potential to ameliorate some of the negative effects of acidification but may also make matters worse. The integrative morphology-ecomechanics approach is key to understanding how marine biominerals will perform in the face of changing climate.