Marine diatoms are key components of the planetary ocean, playing crucial roles in trophic networks: fixing carbon, producing fatty acids (FA) that cannot be synthesized de novo by higher trophic organisms. To better comprehend how the combined action of climatic change influences the dietary value and the impacts on the upper trophic levels, we used a 2 × 2 factorial experiment to investigate how the FA profiles of Skeletonema marinoi changed in response to the individual and combined effects of warming (7, 19°C) and acidification (400, 1 000 ppm CO2). Three S. marinoi strains were exposed for ~ 40 weeks to ambient conditions, warming, acidification and their combination and analyzed for FA profiles, focusing on polyunsaturated (PUFA), omega-3 and omega-6 FA. We found that omega-3 FA increased under warming exposure, while acidification alone led to lower omega-3/omega-6 ratios. In contrast, the ratios increased under warming, alone or coupled with acidification, in all three strains, indicating better food quality for higher trophic levels. Our results suggest the long-term exposure to both drivers will help the marine diatoms to acclimatize to their combined effects, allowing them to buffer the changes brought by warming and ocean acidification.
Continue reading ‘Warming and acidification alter essential fatty acid profiles in marine diatom Skeletonema marinoi’Posts Tagged 'molecular biology'
Warming and acidification alter essential fatty acid profiles in marine diatom Skeletonema marinoi
Published 28 July 2026 Science Leave a CommentTags: biological response, BRcommunity, laboratory, molecular biology, North Atlantic, physiology, phytoplankton
Response of Zostera japonica rhizosphere bacteria to ocean acidification
Published 24 July 2026 Science Leave a CommentTags: biological response, community composition, laboratory, molecular biology, North Pacific, otherprocess, phanerogams, photosynthesis, prokaryotes
Abstract
Amidst global climate change, the escalating atmospheric CO2 levels have intensified ocean acidification (OA), significantly impacting the structure and function of marine ecosystems. Seagrass beds, representative nearshore ecosystems, play a pivotal role in carbon sequestration, biodiversity preservation, and nearshore environmental equilibrium. Rhizosphere microorganisms within seagrass beds, essential components of the ecosystem, drive material cycling and energy flow. Their community structure and functions demonstrate heightened sensitivity to environmental variations. While previous studies have primarily focused on the effects of ocean acidification on seagrass hosts, limited attention has been given to the rhizosphere. Therefore, this study selected Zostera japonica as the focal species and systematically evaluated changes in the structure and function of the rhizosphere bacterial community across varying acidification levels (400 ppm, 1,000 ppm, 2,000 ppm CO2) within an ocean acidification context. The results revealed a significant decline in the richness and diversity of the rhizosphere bacterial community under acidification, accompanied by shifts in community composition characterized by an increase in the relative abundance of Bacteroidota and Tenacibaculum with escalating acidification levels. In high acidification conditions, bacterial network interactions exhibited a trend toward simplification; yet the number of key taxonomic units increases, and there was a shift in community assembly from stochastic to deterministic processes. Functional predictions indicated the enhancement of microbial carbon sequestration and nitrogen fixation under acidification, while denitrification and specific sulfur metabolism pathways were inhibited. This implies that in acidified environments, the rhizosphere bacterial community may enhance carbon and nitrogen fixation to uphold nutrient supply.
Importance
Against the background of escalating global climate change and ocean acidification, seagrass beds, as crucial blue carbon sink ecosystems, face formidable challenges to their ecological functions and stability. Rhizosphere microorganisms of seagrasses, serving as the “second genome” of the seagrass host, play a central role in material cycling, nutrient supply, and system stability within seagrass beds. They are a key biological component that supports seagrass adaptation to environmental changes. Therefore, investigating the response and adaptation mechanisms of seagrass rhizosphere bacterial communities under ocean acidification is essential for deepening our understanding of the stability and resilience of seagrass bed ecosystems.
Continue reading ‘Response of Zostera japonica rhizosphere bacteria to ocean acidification’The molecular footprint of global change in Antarctic coral
Published 21 July 2026 Science Leave a CommentTags: Antarctic, biological response, BRcommunity, corals, laboratory, molecular biology, multiple factors, physiology, temperature
Anthropogenic CO2 emissions are altering marine ecosystems through two interconnected processes: climate change and ocean acidification, both of which are particularly affecting the Southern Ocean. However, the molecular responses of cold-water corals to these stressors remain poorly understood. In this study, we investigated the transcriptomic response of the Antarctic coral Malacobelemnon daytoni exposed to ocean acidification (pH ~7.7; LpH) and elevated temperatures (+2°C and +4°C above ambient; T1 and T2, respectively) under controlled laboratory conditions. Using high-throughput RNA sequencing (RNA-Seq), we compared gene expression profiles across six treatments, including a control (pH ~8.1, CpH; 0–1°C; CT), acidification, warming, and their combinations. Principal component analysis revealed treatment-specific clustering and greater transcriptomic dispersion under LpH conditions. Differential expression analysis identified between 475 and 767 differentially expressed genes (DEGs), with the strongest transcriptional responses observed under combined stress conditions (LpH + T1 and LpH + T2). Combined exposure to ocean acidification and warming elicited the largest gene expression response, suggesting enhanced, potentially non-additive effects of multiple stressors. Functional enrichment analyses revealed differential regulation of genes associated with protein folding, signal transduction, energy metabolism, oxidative stress, and regulation of cell death. Our findings demonstrate that Malacobelemnon daytoni exhibits complex, treatment-dependent gene expression responses to environmental stressors. These results highlight the capacity of this Antarctic octocoral to mount molecular responses to projected future ocean conditions while also emphasizing its potential vulnerability to the interacting effects of ocean warming and acidification.
Continue reading ‘The molecular footprint of global change in Antarctic coral’Strong effects of sun exposure on oyster shell corrosion and compensatory calcification: a factor confounding coastal acidification responses
Published 13 July 2026 Science ClosedTags: biological response, calcification, field, laboratory, molecular biology, mollusks, North Pacific, physiology
The dynamics of calcium carbonate structures in marine organisms (skeletons and shells) has become increasingly important due to heightened interest in marine environmental acidification. Research into molluscan shell corrosion and calcification in response to acidification is typically carried out in laboratory-controlled settings, which often overlooks the intricate interactions found in natural environments. Mollusks inhabiting intertidal zones are especially susceptible to intense shell weathering caused by tidal cycles of heating, cooling, wetting, and drying, exacerbated by solar radiation during periods of air exposure. We investigated the effect of sun exposure (solar radiative heating) on both outer shell corrosion and inner shell compensatory calcification in the tropical oyster, Saccostrea scyphophilla. Shell properties were compared between oysters from neighboring populations in sun-exposed and shaded habitats. Habitat temperatures were measured using iButtons, and right shell valve corrosion was quantified. Compensatory calcification was assessed through measurements of shell thickness, shell density, shell compression strength, and mineralogical properties. Our results revealed that oysters in the sun that experience global irradiance, higher temperature peaks and broader daily temperature ranges (averaging an increase of 10 °C) show considerably greater outer shell surface corrosion (87%) compared to shaded oysters (31%) that experience only diffuse irradiance. Sun-exposed shells also become thickened in the midsection and around the adductor muscle, and they are slightly stronger, indicating compensation for the outer shell loss. These findings highlight the need for caution when interpreting molluscan shell dynamics based on laboratory marine acidification protocols that fail to account for the many natural environmental factors influencing shell formation and dissolution.
Continue reading ‘Strong effects of sun exposure on oyster shell corrosion and compensatory calcification: a factor confounding coastal acidification responses’Short-term plasticity and long-term transcriptomic rewiring under natural ocean acidification in an ecosystem-relevant sea urchin
Published 1 July 2026 Science ClosedTags: biological response, BRcommunity, echinoderms, laboratory, molecular biology, North Atlantic, vents
Highlights
- Natural CO2 vents reveal transcriptomic responses to chronic ocean acidification.
- Acute low-pH exposure triggers rapid but limited plastic responses in Arbacia lixula.
- Vent-origin Arbacia lixula exhibit extensive metabolic reprogramming and antioxidant activation.
- Low pH supresses biomineralization genes and up-regulates collagen and extracellular matrix pathways.
- Persistence under ocean acidification is associated with energetic trade-offs and skeletal homeostasis.
Abstract
Ocean acidification is reshaping coastal ecosystems as a consequence of anthropogenic CO2 emissions. Natural CO2 vent systems provide valuable analogues for investigating organismal responses to long-term acidified conditions under ecologically realistic scenarios. Here, we examined genome-wide transcriptomic responses of the sea urchin Arbacia lixula, an ecosystem-relevant grazer inhabiting a natural CO2 vent system in La Palma (Canary Islands, Spain). Using RNA sequencing of 24 adults (n = 8 per treatment), we compared: (i) acute experimental exposure of ambient-origin individuals to low pH, (ii) chronic exposure by comparing ambient and vent-origin populations in their native pH conditions, and (iii) a genotype-of-origin comparison under shared low pH. Acute exposure triggered a limited transcriptional response (116 differentially expressed genes, DEG), characterized by activation of ion transport, redox regulation, and NAD-associated metabolism. In contrast, chronically exposed vent-origin urchins showed a tenfold increase in transcriptional changes (1053 DEG), reflecting metabolic reprogramming involving lipid, carbohydrate and amino acid pathways, and strengthened antioxidant capacity. Chronic low-pH exposure was also associated with suppression of biomineralization and developmental genes, alongside strong upregulation of collagen and extracellular matrix–associated genes that may help maintain skeletal performance under reduced carbonate availability. Genotype-of-origin effects (131 DEGs) revealed constitutive differences in metabolic, redox, extracellular matrix, and biomineralization pathways in vent populations. Together, these findings indicate that persistence under natural acidification involves both rapid plastic responses and sustained physiological reorganization, providing mechanistic insight into how calcifying species maintain functional performance under ongoing ocean acidification.
Continue reading ‘Short-term plasticity and long-term transcriptomic rewiring under natural ocean acidification in an ecosystem-relevant sea urchin’Shifts of tentacles-associated prokaryotes of Anemonia viridis along a natural pH gradient
Published 18 June 2026 Science ClosedTags: biological response, BRcommunity, cnidaria, community composition, laboratory, Mediterranean, molecular biology, otherprocess, physiology, prokaryotes, sediment
Highlights
- A. viridis tentacle microbiomes were studied under changing natural pH conditions.
- Notable shifts in the abundance of specific taxa emerged in the acidified sites.
- Differences in seawater emphasized the host’s unique microbial signature.
- Rickettsiales predominance suggested a specialized ecological role in symbiosis.
- Further research is needed to discern the role of microbes for host resilience.
Abstract
Marine hydrothermal vents are extreme environments that naturally select for organisms with strong resistance and the ability to cope with special conditions of acidification. Sea anemones are an interesting example that are able to buffer intracellular pH conditions. In this study, the influence of a natural pH gradient on microbial communities associated with Anemonia viridis (Cnidaria, Anthozoa) tentacles was investigated. We hypothesized that exposure to a natural pH gradient would be associated with changes in the structure and activity of A. viridis-associated microbial communities, potentially contributing to the host’s resilience in hydrothermal environments. Microbial enzymatic activities within anemones’ tentacles were investigated by incubation with fluorogenic compounds. The leucine amino peptidase activity was highest in the tentacles of specimens living in more acidified sites. A microbial biodiversity loss was observed in bacterial symbionts from less acidified to more acidified sites, with a reduction of relative abundance in certain groups (i.e., Planctomycetota, Firmicutes, and Desulfobacterota). Results obtained by a metabarcoding approach provided interesting insights into the taxonomic shifts of the A. viridis holobiont system in naturally acidified environments.
Continue reading ‘Shifts of tentacles-associated prokaryotes of Anemonia viridis along a natural pH gradient’Climate change is redefining tetrodotoxin accumulation and ecological dynamics in pufferfishes
Published 16 June 2026 Science ClosedTags: biological response, fish, molecular biology, performance, physiology, review
Marine pufferfishes are globally distributed and ecologically important organism notable for accumulating tetrodotoxin [TTX], a potent neurotoxin with wide ecological ramifica-tions. Unlike many endogenous defences, TTX in pufferfishes is acquired indirectly via microbial and trophic pathways, linking pufferfish toxicity to the dynamics of marine mi-crobial assemblages and food webs. Anthropogenic climate change principally ocean warming, deoxygenation, and acidification is rapidly reshaping marine environments in ways that are likely to intensify and redistribute TTX exposure. Observational and experimental studies indicate that elevated seawater temperatures favour the proliferation of thermophilic, toxin-producing bacteria [e.g., Vibrio spp.], increase the abundance of toxic prey, and raise TTX burdens in pufferfish tissues seasonally and spatially. Concurrently, warming-driven range shifts have promoted poleward expansions of several tropical and subtropical puffer species, producing novel sympatric assemblages, hybridization events, and “cryptic” toxic phenotypes that complicate species identification and risk assess-ment. These biogeographic rearrangements, together with altered prey communities and microbial composition, reconfigure the trophic pathways by which TTX is transferred and concentrated in higher trophic levels. Early evidence also links multistressor conditions elevated temperature combined with hypoxia or acidification to altered developmental success and changes in toxin allocation during reproduction, suggesting potential popu-lation-level consequences. This review synthesizes current global evidence on cli-mate-linked changes in pufferfish TTX dynamics, integrating microbial ecology, trophic transfer, life-history shifts, and biogeography. We highlight [i] mechanistic pathways by which warming and associated ocean changes increase environmental TTX availability, [ii] how shifting species ranges and hybridization alter toxicity patterns across regions, and [iii] key methodological advances [e.g., high-resolution LC-MS/MS, metagenomics] needed to resolve open questions. We identify critical research gaps long-term field moni-toring, integrated microbial–trophic mapping, and multistressor population studies and recommend synthesis strategies that link environmental monitoring to toxin surveillance. Understanding pufferfish toxification as a climate-sensitive ecological process [not a static species trait] is essential to anticipate how marine toxin landscapes will change in the Anthropocene and to develop timely, science-based monitoring frameworks.
Continue reading ‘Climate change is redefining tetrodotoxin accumulation and ecological dynamics in pufferfishes’Response mechanism of Sepia esculenta larvae under global warming, ocean acidification and salinity fluctuation: Integrated biochemical and transcriptome profiling
Published 12 June 2026 Science ClosedTags: biological response, growth, laboratory, molecular biology, mollusks, North Pacific, physiology, reproduction
Highlights
- Analysis based on global warming, ocean acidification and salinity fluctuation.
- Multi-angle analysis of Sepia esculenta under temperature, pH and salinity stress.
- Different stress enhanced the immune defense and antioxidant defense of S.esculenta.
- The hub genes closely related to stress resistance were identified and screened out.
Abstract
The Sepia esculenta occupies a significant economic proportion in the squid family, and it is also the squid with the largest economic value in the northern sea area of China. With the occurrence of global warming, ocean acidification and ocean salinity fluctuations, it has caused serious negative effects on the development of the S. esculenta artificial breeding industry. Therefore, in the research, we employed weighted gene co-expression network analysis (WGCNA) to investigate the effects of three environmental factors, including salinity, temperature and pH, on the molecular mechanism of S. esculenta larvae, and proved the reliability of transcriptome results through physiological indicators. Enrichment analysis of each module indicated that environmental exposure markedly influenced immune function, oxidative stress responses, and other physiological processes in S. esculenta larvae. Our research elucidates the comprehensive response mechanism of S. esculenta under different environmental stresses, clarifies the significant molecular pathways essential for its growth and development.
Continue reading ‘Response mechanism of Sepia esculenta larvae under global warming, ocean acidification and salinity fluctuation: Integrated biochemical and transcriptome profiling’Ocean acidification effects on larval development and survival in commercially important shellfish
Published 10 June 2026 Science ClosedTags: biological response, fisheries, growth, mitigation, molecular biology, mollusks, mortality, physiology, reproduction, socio-economy
This paper studies the consequences of ocean acidification (OA) on the growth and survival of the larvae of commercially significant shellfish species such as oysters, mussels, and scallops. The authors of the study are particularly concerned with the negative processes of OA with respect to the growth of larvae, shell development, and behavior, which result in decreased survival rates, particularly the consequences of the reduced availability of calcium carbonate on the weakening of shells and larvae, which are preyed upon. The paper also studies the interference with the behavior of larvae, particularly with respect to the adequate detection of sites to settle, which is harmful to recruitment success. Additionally, the study looks at the OA-induced metabolic stress, where the larvae are expected to expend higher energy to maintain homeostasis at the expense of growth and immunity. By focusing on this issue, the paper outlines the OA’s impacts on the shellfish populations and industries. The paper also looks at the available soft measures, such as the implementation of buffering solutions to limit the acidification in hatcheries, the use of genetic selection to incorporate acidification-resistant traits, and coastal management measures to limit local sources of acidification. The paper also suggests some potential new ways to increase the resilience of shellfish stock, including more flexible adaptive aquaculture practices. With commercial shellfish interests emerging, this paper fills some of the more critical gaps in the existing literature and offers insight into the impact of OA on the sustainability of the shellfish industry. It also provides OA mitigation strategies to preserve shellfish stocks in a changing climate.
Continue reading ‘Ocean acidification effects on larval development and survival in commercially important shellfish’Microbial communities associated with two populations of the sponge Chondrilla nucula under present and projected climate conditions in the Aegean Sea
Published 25 May 2026 Science ClosedTags: biological response, BRcommunity, community composition, laboratory, Mediterranean, molecular biology, otherprocess, porifera, prokaryotes
This data paper describes bacterial and fungal communities associated with the sponge Chondrilla nucula collected from two Eastern Mediterranean populations (North and South Aegean Sea) and maintained under controlled common-garden conditions simulating present and projected climate scenarios over a period of 3 months. Microbial composition was characterised using two complementary ribosomal marker approaches: Illumina (MiSeq) sequencing of the 16S rRNA gene for Bacteria and Oxford Nanopore (MinION) sequencing of a long 18S-ITS-28S rRNA fragment for Fungi. A total of 24 sponge libraries (3 climate conditions x 2 populations x 4 biological replicates) along with six control libraries (water from three experimental tanks, extraction and PCR blanks) were constructed for each group of microsymbionts. The resulting reads were processed using custom and publicly available bioinformatic pipelines and databases, followed by initial taxonomic assignment. This dataset represents the first fungal community associated with C. nucula and the first bacterial community for this species from the Aegean Sea.
Continue reading ‘Microbial communities associated with two populations of the sponge Chondrilla nucula under present and projected climate conditions in the Aegean Sea’Carbon allocation strategy of Thalassiosira weissflogii in response to elevated pCO2
Published 25 May 2026 Science ClosedTags: adaptation, biological response, laboratory, molecular biology, otherprocess, photosynthesis, physiology, phytoplankton
Diatoms are of significance in the marine ecosystem, playing a pivotal role in the sustenance of marine life and the transfer of carbon from the surface ocean to deeper waters. Although numerous studies have investigated the effects of elevated carbon dioxide (CO2) on marine diatoms across both short- and long-term adaptation scales, the molecular mechanisms governing chitin metabolism in response to ocean acidification remain poorly understood. In this study, we employed an integrated approach combining transcriptomic, metabolomic, and physiological analyses to examine the marine diatom Thalassiosira weissflogii following 40-day acclimation to high-CO2 conditions. Physiological studies have demonstrated that ocean acidification has the capacity to result in an augmentation of the C/N ratio, chitin content, maximum PSII quantum yield (Fv/Fm), and photosynthetic pigment content of T. weissflogii. Analysis of chlorophyll fluorescence dynamics further demonstrated enhanced primary photochemical efficiency of PSII in the acidified treatment group. Consistent with this, the transcriptome results also showed that the photosynthesis-related pathways were upregulated to meet the increased material and energy requirements after adaptation to elevated CO2 levels. More importantly, it was determined that acidification treatment resulted in the upregulation of chitin synthesis and the downregulation of chitin degradation in T. weissflogii, consequently leading to an augmentation in chitin content. These findings indicate that ocean acidification (high CO2, low pH) prompts T. weissflogii to prioritize the allocation of carbon resources to the synthesis of chitin. The synthesis of chitin may reinforce cell wall formation as an adaptive response to ocean acidification. Our research provides new insights into the marine acidification adaptation strategies of T. weissflogii.
Continue reading ‘Carbon allocation strategy of Thalassiosira weissflogii in response to elevated pCO2’Genome-wide identification and expression analysis of calmodulin and calmodulin-like (CaM and CML) gene family in Magallana gigas
Published 21 May 2026 Science ClosedTags: biological response, laboratory, molecular biology, mollusks
Highlights
- 7 CaM family members and 55 CML family members were identified in Magallana gigas.
- MgCaM and MgCML genes showed tissue-specific and developmental stage-specific expression patterns.
- Distinct expression patterns emerged under heat and acidification stresses.
Abstract
Ca2+ is a multifunctional second messenger that can regulate the activities of hormones and environmental signals related to biotic and abiotic stresses, playing a role in a wide range of cellular processes and influencing almost all aspects of life. In organisms, calmodulin (CaM) and calmodulin-like proteins (CML) can sense and decode the regulatory signals of Ca2+ through the EF-hand (a helix-loop-helix structure) domain. In this study, 7 CaM family members and 55 CML family members were identified in Magallana gigas. All MgCaM and MgCML genes distributed unevenly on 7 chromosomes, with 90% of the genes located on chromosomes 6 and 5. Furthermore, the expression of MgCaMs and MgCMLs was tissue-specific in M. gigas, and most of the genes expressed highly in gill, labial palp, adductor muscle and female gonad. Through the analysis of transcriptome data, it was found that the MgCaM and MgCML genes showed specific expression patterns in response to abiotic stress. When encountering heat-shock stress, different genes responded at different time points. In response to acidification stimulation, genes in the outer edge of mantle could respond to the stimulus obviously. The expression patterns of five representative genes were validated by RT-qPCR under acidification. This study systematically analyzed the characteristics of oyster CaM and CML gene families, revealing their crucial roles in the environmental adaptation mechanisms of M. gigas.
Continue reading ‘Genome-wide identification and expression analysis of calmodulin and calmodulin-like (CaM and CML) gene family in Magallana gigas’Genome-wide characterization of the Pacific oyster Crassostrea gigas SLC4 gene family and expression profiles in response to acidification
Published 20 May 2026 Science ClosedTags: biological response, laboratory, molecular biology, mollusks, reproduction
Highlights
- Eight CgSLC4 genes family members were identified.
- CgSLC4s exhibited tissue-specific and developmentally variable expression patterns.
- CgSLC4 gene family responds to acidification stress in different mantle folds.
- CgSLC4A10-1 shows marked acidification responsiveness, especially in mantle epithelium cell.
Abstract
The solute carrier 4 (SLC4) family represents a category of integral membrane transporters responsible for bicarbonate mediation, which is vital for numerous fundamental biological functions. In this study, eight SLC4 genes were identified and annotated in Crassostrea gigas genome, comprising one member of Cl−/HCO3− exchanger, five genes coding Na+-dependent HCO3− transporters, and two Na+-coupled borate transporter copies, which were located on three chromosomes. In general, the expression of CgSLC4s showed tissue specificity, and differential expression patterns of CgSLC4s was observed at different developmental stages. The CgSLC4 family genes displayed divergent responses to acidification across different mantle folds. Among these family members, CgSLC4A10-1 exhibited the most dramatic and statistically significant expression changes in response to acidification across mantle folds, with fold changes ranging from 0.008-fold down-regulation to 85.95-fold up-regulation. According to the results of RT-qPCR and immunofluorescence, after 14 days of acidification treatment, CgSLC4A10-1 mRNA expression level was significantly increased, immunoblotting signal intensity was also enhanced in the epithelial cells. These results provide a general characterization of the SLC4 gene family in C. gigas, which may provide a systematic overview of the SLC4 gene family in C. gigas, and lay a foundation for future studies to explore its potential involvement in ion homeostasis and acidification adaptation in bivalve mollusks.
Continue reading ‘Genome-wide characterization of the Pacific oyster Crassostrea gigas SLC4 gene family and expression profiles in response to acidification’Coupled ocean warming and acidification reduce shell integrity and bioenergetics in juvenile Mytilus coruscus
Published 7 May 2026 Science ClosedTags: biological response, laboratory, molecular biology, mollusks, morphology, multiple factors, physiology, temperature
Under realistic climate change scenarios, marine bivalves face compounding stressors from concurrent ocean warming and acidification. Research has established the separate effects of these factors; however, the synergy driving physiological adaptation in mollusks has yet to be fully elucidated. We assessed the physiological responses of an ecologically significant mussel, Mytilus coruscus, to 2 mo exposure under varying environmental conditions (25°C/28°C and pH 7.7/8.1). Key metrics included shell properties, flesh weight, antioxidant defenses, bioenergetics, and gene expression. Compared to control groups, experimental groups showed reductions in shell hardness and compressive strength, >10% decrease in flesh weight, and 40-52% suppression of carbonic anhydrase and Ca2+-ATPase activities. Molecular analyses of the mantle tissue demonstrated compromised mitochondrial energy transduction (>40% reduction in ATP6 expression) alongside upregulated stress response markers (>2.1-fold COX3 increase). Notably, cellular energy allocation declined, accompanied by depletion of energy reserves (proteins, lipids, carbohydrates), indicating metabolic prioritization toward stress compensation. These findings elucidate how coupled stressors disrupt homeostasis through multilevel interactions, forcing energy trade-offs between defense mechanisms and growth processes, and confirm the tissue-specific vulnerability of the mantle and individual resilience of bivalves under multifactorial climate change.
Continue reading ‘Coupled ocean warming and acidification reduce shell integrity and bioenergetics in juvenile Mytilus coruscus’Coccolithophore genetic diversity, morphology, and contribution to particulate inorganic carbon production in Western North American coastal waters
Published 27 April 2026 Science ClosedTags: abundance, biogeochemistry, biological response, chemistry, field, molecular biology, morphology, North Pacific, phytoplankton
Coccolithophores, as calcifying phytoplankton, play a critical role in the global carbon cycle by producing calcium carbonate (CaCO3) in the ocean through their calcitic coccoliths. Here we examine Gephyrocapsa huxleyi (formerly Emiliania huxleyi) and related species abundance and genetic diversity along the West Coast of North America from samples taken on the 2021 NOAA West Coast Ocean Acidification (WCOA21) cruise, along the margin from British Columbia, Canada, to San Diego, California, USA. Significant carbonate chemistry gradients were observed across 17 transects, mostly in the onshore-offshore and north-to-south direction. Abundance and morphometrics of Gephyrocapsa spp. was evaluated using real-time PCR of mitochondrial cytochrome c oxidase subunit 3 ( cox3 ) gene and by microscopy. Variation in PIC concentrations, G. huxleyi and related species abundance, and coccosphere thickness were found to be associated with the gradients in carbonate chemistry and nutrient concentrations (phosphate, nitrate, nitrite, ammonium) across stations sampled during the cruise. We identified 5 unique amplicon sequence variants (ASVs) of Gephyrocapsa spp. cox3 that systematically varied in relative abundance across the California Current System. Southern California locations had greater diversity in cox3 sequences than northerly locations. These analyses represent baselines for evaluation of the impacts of future environmental changes in coastal waters along this productive upwelling regime.
Continue reading ‘Coccolithophore genetic diversity, morphology, and contribution to particulate inorganic carbon production in Western North American coastal waters’Ocean acidification induces neuronal hyperexcitation and anxiety-like behaviour in marine medaka via ASIC activation
Published 21 April 2026 Science ClosedTags: biological response, fish, laboratory, molecular biology, performance, physiology
Ocean acidification presents a significant threat to marine life, yet its neurobiological mechanisms remain poorly understood. This study examined how acid-sensing ion channels (ASICs) mediate neuronal excitability and anxiety-like behaviour in marine medaka (Oryzias melastigma) under elevated CO2 concentrations (1000 and 1900 ppm). Transcriptomics revealed early upregulation of asic1a (4 days), while RT-qPCR demonstrated increased asic1a, asic1b, asic2 and asic4a (7 days), with only asic1a sustained at 30 days. Immunofluorescence confirmed heightened Asic2 in emotion-processing brain regions following acidification. Transmission electron microscopy unveiled distinct ultrastructural alterations: widened synaptic clefts, thinned postsynaptic densities, and decreased mitochondrial aspect ratios. Mitochondrial membrane potential assays revealed a reduction in membrane potential in response to acidification. Electrophysiological recordings showed increased neuronal firing count in the dorsolateral telencephalon under acidification, behavioural assessments revealed significant anxiety-like phenotypes, effects that were fully rescued by ASIC inhibition. These results indicated that temporal specificity in ASIC subtype expression in acidification response. The interplay of synaptic and mitochondrial dysfunction, neuronal hyperexcitability, and behavioural alterations suggested acidification impaired both synaptic transmission efficiency and mitochondrial function, destabilizing neural circuits. This study systematically elucidates the neurotoxic effects of ocean acidification on marine fish, providing critical scientific evidence for predicting the ecological impacts of climate change on marine organisms.
Continue reading ‘Ocean acidification induces neuronal hyperexcitation and anxiety-like behaviour in marine medaka via ASIC activation’Coexpression among eastern oyster host and microbiome genes suggests coordinated regulation of calcifying fluid chemistry
Published 13 April 2026 Science ClosedTags: biological response, BRcommunity, laboratory, molecular biology, mollusks, North Atlantic, physiology, prokaryotes
Significance
Oysters and many marine animals build shells by controlling the chemistry of extracellular fluids where minerals form, yet whether microbes in these fluids influence calcification remains unclear. We show that oysters maintain favorable conditions for mineral formation by regulating the carbonate chemistry of the shell-forming fluid, and that resident microbes respond to these changes by expressing nitrogen- and sulfur-cycling genes capable of altering pH, alkalinity, and carbonate availability. Many of these microbial transcripts were tightly correlated with oyster immune and signaling genes, suggesting that host and microbiome processes may be linked within the calcifying environment. These findings point to a host–microbiome interaction in the regulation of calcifying-fluid chemistry that directly links microbial activity to the carbonate chemistry underlying biomineralization.
Abstract
Marine animals that build shells, such as oysters, carefully regulate the chemistry of their internal calcifying fluids, but the molecular mechanisms behind this control, as well as whether microbes play a role in calcification, are poorly understood. To better understand oysters’ molecular mechanisms and the role of their calcifying-fluid microbes, we conducted experiments that simulated a tidal cycle, measured calcifying fluid pH and total dissolved inorganic carbon, and characterized host and microbial gene expression via transcriptomics. These experiments showed that calcifying fluid pH remained relatively stable throughout tidal pH fluctuations, with corresponding increases in oyster transcripts for ion transport and acid–base regulation. These data provide direct evidence that tidal fluctuations drive rapid changes in oyster calcifying fluid chemistry. Most surprisingly, increases in microbial transcripts related to nitrogen and sulfur cycling correlated to higher calcifying fluid DIC, and coexpression network analysis revealed patterns of gene expression that linked oyster immune and neural pathways to microbial redox processes, providing molecular evidence of potential host modulation of microbial metabolism. Together, these results reveal that oysters actively regulate their calcifying fluid pH over short timescales, and the endemic microbiome metabolic responses can yield metabolites that influence calcifying fluid pH, alkalinity, and ultimately calcification. These data offer a perspective on oyster physiological capacity and, most importantly, the potential role of microbes in oyster calcification. In light of ongoing changes in ocean pH and temperature, oysters provide a model for studying animal–microbial responses to environmental acidification and how their interactions may shape biomineralization.
Continue reading ‘Coexpression among eastern oyster host and microbiome genes suggests coordinated regulation of calcifying fluid chemistry’Intracellular acid-base regulation mediates a trade-off between shell and somatic growth in a clam under ocean acidification
Published 9 April 2026 Science ClosedTags: biological response, growth, individualmodeling, laboratory, mesocosms, modeling, molecular biology, mollusks, North Pacific, physiology
Highlights
- Clams actively regulate intracellular pH against ocean acidification via CAc
- RNAi confirms CAc’s essential role in H+ efflux, measured by in vivo SIET.
- A CAc-sAC-NKA network forms a conserved regulatory pathway for acid-base balance.
- DEB model shows this pH defense sustains shell linear growth despite metabolic costs.
SUMMARY
Ocean acidification (OA) is predicted to threaten marine bivalves, casting them as passive victims of changing carbonate chemistry. Contributing to a revised understanding, we identified a conserved mechanism for acid-base regulation that supports intracellular resilience. Using the Manila clam Ruditapes philippinarum as a model, this study demonstrated that intracellular pH (pHi) homeostasis under elevated pCO2 was maintained through cytosolic carbonic anhydrase (CAc)-mediated H+ efflux. A causal link was established by combining in vivo scanning ion-selective electrode technique (SIET) with RNA interference (RNAi), where RpCAc knockdown suppressed H+ efflux and compromised pHi. A coordinated regulatory network involving CAc, soluble adenylyl cyclase (sAC), and Na+/K+-ATPase (NKA) was synergistically upregulated, suggesting an evolved adaptive pathway. Dynamic Energy Budget (DEB) modeling, calibrated with experimental data, revealed that this cellular compensation carries a high energetic cost, leading to a significant reallocation of resources: shell growth was maintained, but somatic growth was severely suppressed. These results elucidate a conserved cytoprotective mechanism that enables short-term tolerance of OA at a substantial somatic cost, redefining resilience to include energetic trade-offs.
Continue reading ‘Intracellular acid-base regulation mediates a trade-off between shell and somatic growth in a clam under ocean acidification’Investigation of the adaptive mechanisms to ocean acidification in Patella species from CO2 vent systems of the Mediterranean Sea
Published 7 April 2026 Science ClosedTags: adaptation, biological response, field, Mediterranean, molecular biology, mollusks, morphology, otherprocess, physiology, respiration, vents
The continuous increase in anthropogenic carbon dioxide (CO2) emissions into the atmosphere is one of the main factors contributing to ocean acidification (OA). In fact, CO2 is partially absorbed by the oceans, where it alters carbonate chemistry and seawater pH, which is expected to decrease from the current level of 8.1 to 7.7 by 2100. OA exerts harmful impacts primarily on calcifying organisms, as it affects the availability of carbonates, which makes their calcareous structures thinner and more fragile. Moreover, several studies have described the detrimental effects of OA across many marine taxa, affecting important physiological and metabolic mechanisms. On the other hand, research conducted at CO2 vent systems, which are volcanic naturally acidified sites, showed that several organisms can survive under acidified conditions through specific tolerance and/or adaptive strategies. Among these organisms, the gastropod Patella spp. is one of the few calcifiers capable of inhabiting naturally acidified sites, such as the Castello Aragonese vent systems at Ischia Island and the San Giorgio vent systems at Sicily Island. Nonetheless, the complex mechanisms that allow survival and potential adaptation of these organisms to natural OA conditions need to be understood. Therefore, this PhD study aimed at investigating the potential molecular, physiological, metabolic, genetic, and epigenetic mechanisms that enable these organisms to tolerate and survive under OA conditions through a stepwise approach. Specifically, this PhD research attempted to answer the following questions: • Does OA entail a stressful condition in resident populations of Patella spp. living at reduced pH conditions, thereby affecting their overall well-being and health status? • Are there specific physiological, metabolic, and biochemical mechanisms that contribute in defining tolerance to OA? • Are limpets genetically adapted to OA? • Is DNA methylation contributing to promote tolerance to OA in limpets? • What is the role of environmental conditions in shaping the response to OA? The first chapter of this thesis considered three Patella species (P. caerulea, P. rustica, and P. ulyssiponensis) collected from the CO2 vent systems of the Castello Aragonese (Ischia Island). This vent system exhibits a natural acidification gradient ranging from ambient pH (N1: pH = 8.1), to intermediate pH (N2: pH = 7.7), and to extremely low pH (N3: pH < 7.4). Resident populations were collected along the gradient and at San Pietro, an additional ambient pH site (pH = 8.1), located at a distance of 4 km from the Castello vent. In addition, a 30-day in situ transplant experiment was conducted using P. caerulea, in order to evaluate the short-term responses induced by OA. Morphometric traits, such as shell length, height, width, and soft-tissue weight, were measured, and a set of biomarkers related to antioxidant system, energy metabolism, neurotoxicity, and biomineralization was applied. For resident populations, P. caerulea showed increased size and energy reserves at the extremely acidified site, likely related to a shift from erect calcified algae to biofilm, or to reduced competition and/or predatory pressure under acidified conditions. Biochemical endpoints measured in both P. caerulea and P. ulyssiponensis were not modified by OA. Conversely, P. rustica exhibited significant modulation of nearly all biochemical parameters, likely due to its different position on the rocky shore, which makes this species more exposed to tidal fluctuations and therefore to an additional source of disturbance, besides OA. Short-term exposure of P. caerulea to OA resulted in a decrease in protein content and an increase in glycogen content at the extremely acidified site, with the induction of superoxide dismutase and glutathione-S-transferase activities at intermediate pH, suggesting the activation of compensatory mechanisms to cope with reduced pH conditions. Overall, results revealed a distinct response to OA of the three species of Patella. Moreover, the increased size and energy-related endpoints observed in P. caerulea and P. rustica highlighted the need to further investigate energy metabolism aspects, in order to better understand the trade-offs between compensatory mechanisms and the energetic cost underlying tolerance to OA. Based on these evidences, the second chapter focused exclusively on P. caerulea, with the aim of deeply investigating metabolic and physiological stress-responses, comparing resident populations of the Castello Aragonese vent systems and transplanted organisms, similarly to the first chapter. Respiration and ammonia excretion rates were measured four times across the year. Additionally, untargeted metabolomics analyses were performed to investigate metabolic pathways potentially involved in response to OA. Only during summer, OA increased respiration rate in limpets from the most acidified site, while simultaneously reduced excretion rates, likely to allocate more energy resources to face the increasing temperature, besides OA. Furthermore, both resident and transplanted populations up-regulated carnitine metabolism, suggesting that OA induced an increase of energy production through β-oxidation and subsequent Krebs cycles. Moreover, several metabolites involved in osmoregulation, oxidative stress, and nucleic acid mechanisms were increased. Overall, results seem to confirm the presence of negative effects and of an energetic cost underpinning tolerance to OA. The third and final chapter investigated the potential influence of phenotypic plasticity, genetic adaptation, and DNA methylation in tolerance to OA in adult and juvenile populations of P. caerulea collected from two CO2 vent systems of the Mediterranean Sea. Adult and juvenile specimens were sampled along the acidification gradient of the Castello Aragonese vent systems of Ischia Island (San Pietro/N1: pH = 8.1; N2: pH = 7.7; N3: pH < 7.4) and from the San Giorgio vent systems of Sicily Island (Patti: pH = 8.1; San Giorgio: pH = 7.8). Following genomic DNA extractions from foot tissue and individual libraries preparation with the NEB Next® Enzymatic Methyl-seq Kit, samples were sequenced on the Illumina NovaSeq 6000 sequencer. Data processing and analyses were conducted on Euler platform mainly using biscuit tool, which enabled to simultaneously extract genomic and epigenomic information from DNA methylation sequencing. Population genomics and epigenomics analyses revealed divergent patterns between the Ischia and Sicily populations. Populations from the Ischia vent revealed marked signs of genomic differentiation, particularly in adults from the intermediate and extremely low pH sites, while reduced differences in DNA methylation levels were detected, especially in adults. These findings suggest a strong signature of purifying selection acting on standing genetic variation, through a within-generation response, likely driven by the more pronounced pH fluctuations occurring at these sites. Conversely, no genomic differentiation was observed between the Sicily populations, but greater differences in DNA methylation were detected between acidified and non-acidified sites at both adult and juvenile stages. These results revealed that this epigenetic mechanism, rather than genomic changes, may play a key role in the response to the milder pH variations of this vent and potentially enhance organisms’ tolerance to OA. In conclusion, this PhD project investigated tolerance to OA in limpets through a holistic approach that, for the first time, integrated morphological, physiological, metabolic, biochemical, genetic, and epigenetic analyses. Overall, findings revealed that Patella spp. has the ability to survive under acidified conditions even though with a physiological and metabolic cost, which could be partially compensated by more favorable environmental conditions. This study further highlights the importance of conducting research in naturally acidified environments, since it allows to formulate more realistic hypotheses about the ability of marine organisms to persist in future changing oceans.
Continue reading ‘Investigation of the adaptive mechanisms to ocean acidification in Patella species from CO2 vent systems of the Mediterranean Sea’Tolerance to future elevated CO2 conditions in sablefish (Anoplopoma fimbria), a deep-water benthic dwelling fish species
Published 26 March 2026 Science ClosedTags: biological response, fish, laboratory, molecular biology, North Pacific, performance, physiology
Numerous studies have found that elevated CO2 levels in marine waters induced significant physiological and behavioral effects in fish. In an earlier study of coho salmon (Oncorhynchus kisutch), we observed that elevated CO2 exposure impaired signaling in the olfactory bulb, through a mechanism likely involving interference of gamma-aminobutyric acid (GABA) signaling. However, the effects of elevated CO2 may be species-specific, and there have been few studies addressing the effects of elevated CO2 on benthic fish. In the current study, we investigated the effects of elevated CO2 exposures on the deep-water benthic species, sablefish (Anoplopoma fimbria). Sablefish were exposed to three different levels of CO2 (700, 1600 and 2700 µatm) for two weeks, followed by behavioral, neurophysiological and gene expression analysis of the olfactory system. Analysis of behaviors mediated by food odors, including swimming activity and food strikes did not differ between fish maintained under elevated or control CO2 conditions. Similarly, electro-olfactogram recordings of odorant signaling did not differ among treatment and controls. mRNA expression patterns of olfactory bulb genes that were altered in coho salmon exposed to elevated CO2 levels, were similarly examined in sablefish. Sablefish mRNAs encoding genes involved in GABA-mediated olfactory bulb signaling were generally unaffected by high CO2, but aldh9a1, an enzyme involved in the synthesis of GABA, was elevated by high CO2. The results of our study contrast other studies demonstrating adverse effects of elevated CO2 in pelagic fish, but support differences among fish species to susceptibility to elevated CO2, potentially associated with life history traits.
Continue reading ‘Tolerance to future elevated CO2 conditions in sablefish (Anoplopoma fimbria), a deep-water benthic dwelling fish species’
