Pacific geoduck (Panopea generosa) resilience to natural pH variation

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

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

Proteomic Applications in Aquatic Environment Studies

Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.

Acclimatory gene expression of primed clams enhances robustness to elevated pCO2

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

Seagrass-driven changes in carbonate chemistry enhance oyster shell growth

Quantifying the strength of non-trophic interactions exerted by foundation species is critical to understanding how natural communities respond to environmental stress. In the case of ocean acidification (OA), submerged marine macrophytes, such as seagrasses, may create local areas of elevated pH due to their capacity to sequester dissolved inorganic carbon through photosynthesis. However, although seagrasses may increase seawater pH during the day, they can also decrease pH at night due to respiration. Therefore, it remains unclear how consequences of such diel fluctuations may unfold for organisms vulnerable to OA. We established mesocosms containing different levels of seagrass biomass (Zostera marina) to create a gradient of carbonate chemistry conditions and explored consequences for growth of juvenile and adult oysters (Crassostrea gigas), a non-native species widely used in aquaculture that can co-occur, and is often grown, in proximity to seagrass beds. In particular, we investigated whether increased diel fluctuations in pH due to seagrass metabolism affected oyster growth. Seagrasses increased daytime pH up to 0.4 units but had little effect on nighttime pH (reductions less than 0.02 units). Thus, both the average pH and the amplitude of diel pH fluctuations increased with greater seagrass biomass. The highest seagrass biomass increased oyster shell growth rate (mm day^-1) up to 40%. Oyster somatic tissue weight and oyster condition index exhibited a different pattern, peaking at intermediate levels of seagrass biomass. This work demonstrates the ability of seagrasses to facilitate oyster calcification and illustrates how non-trophic metabolic interactions can modulate effects of environmental change.

Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products

This review presents the primary applications of various proteomic strategies to evaluate the impact of farming conditions on food quality and safety in aquaculture products. Aquaculture is a quickly growing sector that represents 47% of total fish production. Food quality, dietary management, fish welfare, the stress response, food safety, and antibiotic resistance, which are covered by this review, are among the primary topics in which proteomic techniques and strategies are being successfully applied. The review concludes by outlining future directions and potential perspectives.

Hemocyte cell types of the Cortes Geoduck, Panopea globosa (Dall 1898), from the Gulf of California, Mexico

The geoduck Panopea globosa is an endemic and economic valuable species from the Mexican Northwest coast whose biology has been little studied. No information exists about their hemocytes to date, which is highly important to assess the welfare of wild and cultured organisms. In this study, hemocytes of adult P. globosa were characterized at the morphological, ultrastructural and functional level. The mean number of hemocytes in the hemolymph of P. globosa was 6 × 10⁵ ± 2 × 10⁵ cells mL^-1. The cells were identified as granulocytes (Gr) and hyalinocytes (H). The former accounted for 28% of adhered cells in the hemolymph, measured 6-18 μm, showed numerous basophilic granules in the cytoplasm, with round and eccentric nuclei, and a nucleus:cytoplasm ratio of 0.44 ± 0.01. Hyalinocytes were the most abundant cells in the hemolymph of P. globosa (72% adhered cells) and were subdivided, according to their size, in small (Hs) 4-12 μm and large (HL) 6-18 μm. Hyalinocytes were eosinophilic round or ovoid cells with a central or eccentric nucleus, few or no granules in the cytoplasm and similar nucleus:cytoplasm ratio (Hs: 0.63 and HL: 061). Lysosomes and lipids were observed in Gr, while carbohydrates were the most abundant energy substrate in H. Both hemocytic cell types, mainly Gr, were capable to ingest particles and yield superoxide (P > 0.05). The present study shows for the first time the cell types, abundance and immune activities of hemocytes present in the hemolymph of P. globosa. This information provides a useful baseline to carry out further research on the cellular immune response of the clam to potential pathogens or changes in environmental factors.

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.

Comparative physiology and aquaculture: Toward Omics-enabled improvement of aquatic animal health and sustainable production

Omics-technologies have revolutionized biomedical research over the past two decades, and are now poised to play a transformative role in aquaculture. This article serves as an introduction to a Virtual Special Issue of Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics (CBPD), with the objective to showcase the state-of-the-science for Omics in aquaculture. In this editorial, we describe the role that Omics can play in aquaculture, and provide a synopsis for each of the Special Issue articles that use these technologies to improve aquaculture practices. Current genomic resources available for some aquaculture species are also described. The number of datasets is impressive for species such as Atlantic salmon and rainbow trout, totaling in the thousands (NCBI Gene Expression Omnibus and Sequence Read Archive). We present a conceptual framework that describes how Omics can be leveraged to understand complex responses of aquatic animals in culture for relevant physiological outcomes, such as fecundity, growth, and immunity. Lastly, knowledge gaps and new directions are identified to address current obstacles in aquaculture. Articles in this Special Issue on aquaculture in CBPD highlight the diversity and scope of Omics in aquaculture. As the technology becomes more cost-effective, it is anticipated that genomics, transcriptomics, proteomics, metabolomics and lipidomics will play increasingly important roles in stock diagnostics (e.g. genetics, health, performance). The timing is right, as global concerns are reaching critical levels over food availability/security and water restrictions for humankind.