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

Ocean acidification aggravates the toxicity of deltamethrin in Haliotis discus hannai: Insights from immune response, histopathology and physiological responses

Ocean acidification (OA) and other environmental factors can collectively affect marine organisms. Deltamethrin (DM), a type II pyrethroid insecticide, has been widely detected in coastal and estuarine areas, while little attention has been given to the combined effects of DM and OA. In this study, Haliotis discus hannai was exposed to three pH levels (8.1, 7.7 and 7.4) and three DM nominal concentrations (0 μg/L, 0.6 μg/L and 6 μg/L) for 14 and 28 days. The results indicated that experimental acidification and/or DM exposure led to impaired immune function and pathological damage. Additionally, acidified conditions and DM exposure induced oxidative stress, and gills are more sensitive than digestive glands. With increasing pCO2 and DM nominal concentrations, superoxide dismutase (SOD) activity decreased, whereas catalase (CAT) and glutathione S-transferase (GST) activities increased in the gills. Moreover, the expression levels of Toll-like receptor (TLR) pathway-related genes were upregulated after exposure. Integrated biomarker response (IBR) analysis proved that acidified conditions and/or DM detrimentally affected the overall fitness of H. discus hannai, and co-exposure to experimental acidification and DM was the most stressful condition. This study emphasizes the necessity of incorporating OA in future pollutant environmental assessments to better elucidate the risks of environmental disturbance.

Development and validation of a 66K SNP array for the hard clam (Mercenaria mercenaria)

BACKGROUND

The hard clam (Mercenaria mercenaria), a marine bivalve distributed along the U.S. eastern seaboard, supports a significant shellfish industry. Overharvest in the 1970s and 1980s led to a reduction in landings. While the transition of industry from wild harvest to aquaculture since that time has enhanced production, it has also exacerbated challenges such as disease outbreaks. In this study, we developed and validated a 66K SNP array designed to advance genetic studies and improve breeding programs in the hard clam, focusing particularly on the development of markers that could be useful in understanding disease resistance and environmental adaptability.

RESULTS

Whole-genome resequencing of 84 individual clam samples and 277 pooled clam libraries yielded over 305 million SNPs, which were filtered down to a set of 370,456 SNPs that were used as input for the design of a 66K SNP array. This medium-density array features 66,543 probes targeting coding and non-coding regions, including 70 mitochondrial SNPs, to capture the extensive genetic diversity within the species. The SNPs were distributed evenly throughout the clam genome, with an average interval of 25,641 bp between SNPs. The array incorporates markers for detecting the clam pathogen Mucochytrium quahogii (formerly QPX), enhancing its utility in disease management. Performance evaluation on 1,904 samples demonstrated a 72.7% pass rate with stringent quality control. Concordance testing affirmed the array's repeatability, with an average agreement of allele calls of 99.64% across multiple tissue types, highlighting its reliability. The tissue-specific analysis demonstrated that some tissue types yield better genotyping results than others. Importantly, the array, including its embedded mitochondrial markers, effectively elucidated complex genetic relationships across different clam groups, both wild populations and aquacultured stocks, showcasing its utility for detailed population genetics studies.

CONCLUSIONS

The 66K SNP array is a powerful and robust genotyping tool that offers unprecedented insights into the species' genomic architecture and population dynamics and that can greatly facilitate hard clam selective breeding. It represents an important resource that has the potential to transform clam aquaculture, thereby promoting industry sustainability and ecological and economic resilience.

The molecular response of Mytilus coruscus mantle to shell damage under acute acidified sea water revealed by iTRAQ based quantitative proteomic analysis

Mytilus coruscus is an economically important marine bivalve that lives in estuarine sea areas with seasonal coastal acidification and frequently suffers shell injury in the natural environment. However, the molecular responses and biochemical properties of Mytilus under these conditions are not fully understood. In the present study, we employed tandem mass spectrometry combined with isobaric tagging to identify differentially expressed proteins in the mantle tissue of M. coruscus under different short-term treatments, including shell-complete mussels raised in normal seawater (pH 8.1), shell-damaged mussels raised in normal seawater (pH 8.1), and acidified seawater (pH 7.4). A total of 2694 proteins were identified in the mantle, and analysis of their relative abundance from the three different treatments revealed alterations in the proteins involved in immune regulation, oxidation-reduction processes, protein folding and processing, energy provision, and cytoskeleton. The results obtained by quantitative proteomic analysis of the mantle allowed us to delineate the molecular strategies adopted by M. coruscus in the shell repair process in acidified environments, including an increase in proteins involved in oxidation-reduction processes, protein processing, and cell growth at the expense of proteins involved in immune capacity and energy metabolism. SIGNIFICANCE: The impact of global ocean acidification on calcifying organisms has become a major ecological and environmental problem in the world. Mytilus coruscus is an economically important marine bivalve living in estuary sea area with seasonal coastal acidification, and frequently suffering shell injury in natural environment. Molecular responses of M coruscus under the shell damage and acute acidification is still largely unknown. For this reason, iTRAQ based quantitative proteomic and histological analysis of the mantle from M. coruscus under shell damage and acute acidification were performed, for revealing the proteomic response and possible adaptation mechanism of Mytilus under combined shell damage and acidified sea water, and understanding how the mussel mantle implement a shell-repair process under acidified sea water. Our study provides important data for understanding the shell repair process and proteomic response of Mytilus under ocean acidification, and providing insights into potential adaptation of mussels to future global change.

Ca2+ addition facilitates the shell repair with eggs production of Pomacea canaliculata through biomineralization and food intaking regulation

Pomacea canaliculata was by far one of the most harmful invasive organisms in the world, causing serious harm to aquatic crops and ecosystem. Calcium carbonate is a common component of aquatic environment, which is important for the growth of Pomacea canaliculata. Therefore, the objective of this study was to investigate the response characteristics of P. canaliculata suffered shell breakage to the addition of calcium carbonate in water environment. In this experiment, we explored the effects of calcium carbonate addition on the P. canaliculata shell repair rate, food intake, egg production, shell strength, and calcium content through breaking the snails shell and the addition of calcium carbonate treatment. The results showed that snail broken-shell repaired mostly within 21 days. The snails experienced a significant increase in shell repair rates during earlier days of the treatment, especially for female snails. Food intake of snails exhibited different patterns when their shells were broken and calcium carbonate was added. Shell breakage treatment combined with calcium carbonate addition significantly increased the diameter of snail eggs compared with the control and the calcium carbonate addition treatment without shell-broken snail group. There was no significant difference in shell strength or calcium content of male snails between the treatments. The study suggests that P. canaliculata exhibits a sex-dependent response pattern when subjected to shell damage and calcium carbonate addition. The findings can provide some references to better understand the invasion mechanism and survival strategy of the P. canaliculata.

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.