Diatoms play a pivotal role in global biogeochemical cycling and marine primary productivity, making them ideal model organisms for understanding how phytoplankton respond to environmental fluctuations associated with global climate change. In natural marine systems, diatoms frequently encounter simultaneous variations in carbon and nitrogen availability, yet most previous studies have examined the effects of these factors in isolation. To elucidate the integrated transcriptional mechanisms underlying diatom acclimation to coupled carbon–nitrogen (C—N) imbalance, we employed RNA sequencing (RNA‐Seq) to characterize the global transcriptional response of the model diatom Phaeodactylum tricornutum to high CO2 (~2000 μatm) and low nitrogen (10% of nitrogen concentration in f/2 medium) under parallel culture conditions. The results revealed both shared and distinct transcriptional responses between the two treatments. Key genes involved in carbon metabolism, such as phosphoglycerate mutase (PGAM_7) and dihydrolipoamide succinyltransferase (PHATRDRAFT_40430), were significantly upregulated, indicating enhanced glycolytic and TCA cycle activity. In contrast, the Calvin‐cycle enzyme fructose‐1,6‐bisphosphatase (FBPC4) was downregulated. Genes associated with nitrogen assimilation‐including nitrate reductase (PHATRDRAFT_54983), nitrite reductases (PHATRDRAFT_13154, PHATRDRAFT_8155), and ferredoxin–nitrite reductase (PHATRDRAFT_27757)‐were strongly induced under both conditions. Pathway enrichment analysis further indicated the activation of lactic acid fermentation and nitrogen salvage pathways, suggesting a metabolic shift toward energy conservation and nutrient recycling. Collectively, these findings provide an overview of the transcriptional adjustments that enable P. tricornutum to maintain C—N homeostasis under high CO2 and low nitrogen stress, offering new insights into diatom metabolic plasticity under changing ocean conditions.
Continue reading ‘Transcriptomic responses of the marine diatom Phaeodactylum tricornutum to high carbon and low nitrogen stress’Posts Tagged 'molecular biology'
Transcriptomic responses of the marine diatom Phaeodactylum tricornutum to high carbon and low nitrogen stress
Published 23 January 2026 Science ClosedTags: adaptation, biological response, laboratory, molecular biology, multiple factors, nutrients, otherprocess, phytoplankton
Neurometabolic rewiring in squid (Sepioteuthis lessoniana) optic lobes drives behavioral plasticity and visual integration under environmental acidification
Published 20 January 2026 Science ClosedTags: biological response, laboratory, molecular biology, mollusks, North Pacific, performance, physiology
Ocean acidification’s impacts on marine animal behavior have substantial implications for ecosystem stability. Understanding how key predators respond to acidification is crucial for predicting future ocean food web dynamics, yet the underlying neural mechanisms remain poorly understood. Here, we show that prolonged exposure to projected year 2100 acidification conditions substantially impairs predatory behavior in bigfin reef squid (Sepioteuthis lessoniana), a key invertebrate predator. Chronic acidification exposure reduces expression of acetylcholine receptors in optic lobes and alters systemic HCO₃⁻ levels and metabolic rates. Using custom electroretinogram recordings, we find that while basic visual processing remains intact, behavioral impairments likely stem from changes in downstream neural integration pathways. Transcriptomic expression analysis reveals broad reductions in energy metabolism and synaptic signaling under acute exposure, while chronic exposure induces compensatory upregulation of cellular maintenance pathways. Our findings demonstrate that while squids maintain visual capabilities through adaptive mechanisms, the energy-intensive processes of neural integration and behavioral execution are compromised. These results highlight the complex physiological trade-offs marine predators face under ocean acidification, with implications for understanding future shifts in marine ecosystem structure and function.
Continue reading ‘Neurometabolic rewiring in squid (Sepioteuthis lessoniana) optic lobes drives behavioral plasticity and visual integration under environmental acidification’Integrated biochemical profiling, comparative transcriptome and weighted gene co-expression network analysis to explore the response mechanism of global warming and ocean acidification to the stress of Sepia esculenta larvae
Published 16 January 2026 Science ClosedTags: biological response, laboratory, molecular biology, mollusks, multiple factors, North Pacific, physiology, reproduction, temperature
Highlights
- Multi-angle analysis of Sepia esculenta under global warming and ocean acidification.
- Stress enhanced the immune defense and antioxidant defense of S.esculenta.
- The hub genes closely related to stress resistance were identified and screened out.
- Provided a theoretical basis for the breeding of fine varieties and pond culture.
Abstract
The Sepia esculenta has high economic value and nutritional value, and accounts for a high proportion of the catch of cephalopods in China ‘s coastal waters. Global warming and ocean acidification, as major environmental problems currently facing the world, have a serious negative influence on the survival and breeding of S. esculenta. Therefore, in the research, transcriptome sequencing and biochemical quantitative analysis were performed on the larvae of S. esculenta after high temperature, low pH and combined stress at different time points, and the differential expressed genes (DEGs) and response mechanisms were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these DEGs were mainly involved in a large number of immune-related biological processes and signaling pathways, including Immune response、Phagocytosis、Regulation of DNA-templated transcription and Positive regulation of DNA-templated transcription. Then, we further explored the functional relationship between these DEGs by constructing weighted gene co-expression network and protein-protein interaction networks. We identified ten hub genes including HSP90AA1, ALDH1L1, VPS13A, MAPK8IP1 and KDM6A. These hub genes may play an important role in the face of high temperature, low pH and their combined stress at different times. Our findings not only elucidate the molecular response mechanisms of S. esculenta to environmental stress and delineate the key regulatory pathways underlying its adaptation, but also provide a theoretical foundation for advancing pond cultivation.
Continue reading ‘Integrated biochemical profiling, comparative transcriptome and weighted gene co-expression network analysis to explore the response mechanism of global warming and ocean acidification to the stress of Sepia esculenta larvae’Co–occurring aquatic acidification and hypoxia promote methane emissions from estuarine ecosystems
Published 14 January 2026 Science ClosedTags: biological response, laboratory, molecular biology, North Pacific, physiology, sediment
Highlights
- Acidification, hypoxia, and the combined effect enhanced CH4 emission from estuary.
- Acidification and hypoxia exerted contrasting regulatory mechanisms on CH4 emission.
- Acidification raised CH4 release by suppressing methanotrophs more than methanogens.
- Hypoxia preferentially enhanced methanogenic activity over CH4 oxidation.
- Oxygen availability dominated CH4 dynamics under acidification–hypoxia interactions.
Abstract
Estuaries worldwide are experiencing intensifying acidification and hypoxia, driven synergistically by anthropogenic activities and global climate change. Nevertheless, their combined impact on the emissions of the potent greenhouse gas methane (CH4) and its underlying regulatory mechanisms remains poorly understood, undermining our ability to project climate feedbacks. Here, we integrated 13C stable isotope tracing, DNA/mRNA–based qPCR, and amplicon/metagenomic sequencing to unravel how acidification–hypoxia interactions regulate the complex balance between CH4 production and consumption in estuarine sediments. Results showed that aquatic acidification and hypoxia combined to significantly increase CH4 emissions from estuarine sediments (P < 0.05), in a non-additive (antagonistic) manner where oxygen availability was the dominant factor governing this response. Notably, acidification increased CH4 emissions by suppressing methanotrophy more strongly than methanogenesis, whereas hypoxia preferentially stimulated methanogenic activity over CH4 oxidation. These response patterns were further demonstrated by metagenomic sequencing and mRNA-based quantitative PCR analyses, which revealed coordinated shifts in both the relative abundance and transcriptional activity of key functional genes. These findings uncover a previously overlooked mechanism whereby the worldwide co-occurrence of acidification and hypoxia in estuarine ecosystems jointly promote CH4 emissions, providing a scientific basis for improving predictive models of the global CH4 cycle and its climate feedbacks under combined anthropogenic and climatic stressors.
Continue reading ‘Co–occurring aquatic acidification and hypoxia promote methane emissions from estuarine ecosystems’Assessing impacts of extreme climate and weather events on endangered pearl oysters Pinctada maxima
Published 13 January 2026 Science ClosedTags: biological response, laboratory, molecular biology, mollusks, multiple factors, North Pacific, physiology, reproduction, temperature
Extreme climate and weather events in the ocean, especially ocean acidification (OA) and marine heatwaves (MHWs), have strikingly accelerated in the past decades, yet their compound consequences remain poorly understood. The pearl oyster (Pinctada maxima), an endangered keystone species in Indo-Pacific reef ecosystems, is highly vulnerable to such events. Here, we assessed how OA-stressed P. maxima juveniles responded to MHWs (+3 °C), based on a total of 100 individuals exposed to two weeks. Oysters reared at pH 7.7 significantly increased activities of energy-metabolizing enzymes (T-ATP and NKA) in response to MHWs, whereas both enzymes significantly decreased, albeit CMA increased, at pH 7.4. MHWs significantly depressed antioxidant enzyme activities, such as SOD at both pH levels, resulting in elevated MDA levels indicative of lipid peroxidation. Contrasting responses of immune enzymes (ACP and AKP) to MHWs were seen in oysters grown under moderately and severely acidified conditions. MHWs, also, significantly depressed expression levels of key genes related to cellular metabolism (ATP1A, ATP1B, ND5, ATPeV1F and ATPeF1A) and those associated with antioxidant defence (SOD, SOD1, SOD2, Hsp70, Hsp90 and CAT), in particular when stressed at pH 7.4. Taken together, our findings suggest that intensifying MHWs can constrain the ability of P. maxima to cope with OA and likely accelerate further population decline in this era of unprecedented climate change.
Continue reading ‘Assessing impacts of extreme climate and weather events on endangered pearl oysters Pinctada maxima’Physiological and transcriptomic responses of a harmful algal bloom-causing dinoflagellate Karenia mikimotoi to multiple environmental factors
Published 12 January 2026 Science ClosedTags: biological response, growth, laboratory, molecular biology, multiple factors, North Pacific, nutrients, photosynthesis, physiology, phytoplankton, temperature
Highlights
- Elevated temperature was the primary factor significantly reducing K. mikimotoi growth and photosynthesis.
- Increased pCO₂ and high N: P ratios partially mitigated thermal stress induced by elevated temperature.
- K. mikimotoi consistently up-regulated energy and lipid metabolism to cope with environmental stressors irrespective of treatment.
- K. mikimotoi may persist and even thrive under multiple stressors, subsequently influencing productivity and biogeochemical cycles.
Abstract
Dinoflagellates play a crucial role in marine food webs and biogeochemical cycles, yet they are increasingly affected by global environmental changes. While there is limited understanding of their response to individual stressors projected under future oceanic conditions, their response to multiple concurrent environmental stressors remains inadequately explored. This study investigated the singular and interactive effects of elevated temperature (26 °C vs. 22 °C), increased pCO2 (1000 μatm vs. 400 μatm), and a high nitrogen-to-phosphorus ratio (N:P = 180:1 vs. 40:1) on the harmful algal bloom-forming dinoflagellate Karenia mikimotoi over a 40-day exposure period. Among these factors, elevated temperature exerted the most pronounced influence, markedly reducing the cell growth rate and photosynthesis while simultaneously increasing the particulate organic matter content and antioxidant level. Transcriptomic analyses indicated that elevated temperature enhanced the expression of genes associated with oxidative stress, suggesting a potential defense mechanism against thermal stress. Notably, increased pCO2 and a high N:P ratio appeared to mitigate thermal stress to some extent. Irrespective of the treatment, K. mikimotoi demonstrated a consistent response strategy characterized by the synergistic upregulation of energy metabolism and lipid biosynthesis pathways, coordinated by the modulation of both upstream and downstream genes in the tricarboxylic acid cycle. This metabolic reprogramming likely facilitates a more efficient allocation of energy, thereby enhancing the resilience of K. mikimotoi to environmental stress. This study underscores the interactive effects of multiple stressors on marine dinoflagellates, highlighting that elevated temperature is the most critical factor affecting dinoflagellates in future oceanic environments.
Continue reading ‘Physiological and transcriptomic responses of a harmful algal bloom-causing dinoflagellate Karenia mikimotoi to multiple environmental factors’Acute CO2 toxicity and the effects of seawater acidification on health status, histopathology, immunity and disease resistance in Asian Seabass (Lates calcarifer)
Published 12 January 2026 Science ClosedTags: biological response, fish, laboratory, molecular biology, mortality, physiology, reproduction
Carbon dioxide capture and storage (CCS) is a technology that can be used to reduce carbon dioxide (CO2) emissions generated by both natural and anthropogenic industrial processes, particularly petroleum production. To mimic and investigate the effects of CO2 leakage that may result from CCS, the acute toxicity of seawater acidification induced by continuous CO2 injection was studied in Asian seabass (Lates calcarifer) fry under static bioassay conditions. Fry (0.828 ± 0.22 g) were exposed to seawater with different pH levels (5.5, 6.0, 6.5, 7.5, and 8.3). Rapid and 100% mortality within 15 min was observed in the pH 5.5 exposure group, while mortality rates ranging from 10.00–41.67% were recorded at 6–96 h in the pH 6.0 exposure group; no mortality was noted in the other pH exposure groups. According to these mortality data, the median lethal concentration at 96 h (96 h LC50) was determined to be a pH of 5.884. Interestingly, after exposure to seawater with pH levels of 5.5 and 6.0, histopathological alterations in the skin, gills, trunk kidney and liver were evident. Additionally, some water quality parameters, especially dissolved oxygen (DO) levels, alkalinity, ammonia levels, and nitrite levels, vary depending on the pH. To further investigate the effects of seawater with pH levels of 8.3 and 5.884 (96 h LC50) and 6.5 (10% safety level) on health status, immune responses and disease susceptibility, fingerling fish (21.25 ± 3.89 g) were studied. Unexpectedly, fish exposed to seawater with a pH of 5.884 rapidly lost muscle control and gradually died, reaching 100% mortality within 24 h, and all response analyses were aborted. Interestingly, with the exception of hematocrit and some immune parameters, various serum innate immune indices, blood biochemistry parameters and immune-related gene expression patterns were similar in fish exposed to seawater with pH levels of 8.3 and 6.5. Additionally, fish were challenged with 0 (control), 1 × 107 and 1 × 109 CFU/mL Vibrio vulnificus, and fish in seawater with a pH level of 6.5 showed a higher sensitivity to 1 × 109 CFU/mL Vibrio vulnificus than fish in seawater with a pH level of 8.3, with mortality rates of 71.24% and 25.44%, respectively (p < 0.05). These findings enhance the understanding of the toxicity effects of seawater acidification caused by CO2, which will be useful for further assessing the site-specific effects of CCS projects.
Continue reading ‘Acute CO2 toxicity and the effects of seawater acidification on health status, histopathology, immunity and disease resistance in Asian Seabass (Lates calcarifer)’Short-term focus: phased response of Zostera marina seedlings to the combined stress of marine heatwave and ocean acidification
Published 25 December 2025 Science ClosedTags: biological response, laboratory, molecular biology, morphology, multiple factors, North Pacific, phanerogams, physiology, temperature
Marine heat wave (MHW) and ocean acidification (OA) caused by global climate change occur frequently and intensify, which cause damage to the stability of seagrass bed. However, the understanding of the phased-impacts of sudden temperature and acidification changes on seagrass is limited. The study conducted phenomic, transcriptomic and metabolomic analyses to investigate the short-term response mechanisms of Zostera marina seedlings to sudden temperature and acidification incerease. The results showed that Z. marina seedlings activated an integrated metabolic response involving fatty acid metabolism, carbohydrate metabolism and amino acid metabolism to modulate cell membrane properties, enhance thermotolerance and maintain developmental stability. What is noteworthy is that the continuous high expression of the ABC transporters play a crucial role in resisting stress. The study is helpful to clarify the short-term phased response of Z. marina seedlings to the combination of MHW and OA, and have significant importance for the protection and restoration of seagrass beds.
Continue reading ‘Short-term focus: phased response of Zostera marina seedlings to the combined stress of marine heatwave and ocean acidification’Multifactorial neural disruption in the brain of the Senegalese Sole (Solea senegalensis) under ocean acidification
Published 9 December 2025 Science ClosedTags: biological response, fish, laboratory, molecular biology, North Atlantic, physiology
Global ocean acidification, driven by rising atmospheric CO2, is threatening marine ecosystems and biodiversity, with increasing evidence of its disruptive effects on fish neurobiology and behaviour, yet the mechanisms underpinning its impact on fish neurobiology remain unresolved. Here, we reveal how chronic exposure to future-predicted CO2 levels disrupts brain function in the marine teleost Solea senegalensis, a species with functionally distinct olfactory organs. Using an integrative approach combining electrophysiology, immunohistochemistry, and transcriptomics, we demonstrate that elevated CO2 conditions induce a complex multifaceted disruption in brain physiology. Notably, our findings conflict with the widely held GABAA receptor reversal hypothesis; we observed increased Cl- and CO2 in cerebrospinal fluid and suppressed neural excitability, rather than the predicted loss of Cl- and heightened excitatory signalling. Immunohistochemistry further revealed reduced expression of glial fibrillary acidic protein across multiple brain regions, suggesting glial impairment. Furthermore, transcriptomic profiling of the olfactory bulb uncovered immune modulation, downregulation of neural excitability genes, and upregulation of neuroplasticity, ciliary, and anti-inflammatory pathways, hallmarks of cellular stress adaptation. Notably, genes involved in circadian regulation and thyroid signalling were also dysregulated, pointing to broader neuroendocrine disruption. These findings challenge current relatively simple models of ocean acidification impact and unveil a complex cascade of central and peripheral alterations, including enhanced GABAergic inhibition, immune shifts, glial dysfunction, and disrupted timekeeping mechanisms, likely contributing to the behavioural impairments observed under high CO₂. Challenging current models, our work highlights the need for integrative neurophysiological frameworks to predict marine fish resilience and vulnerability in a changing ocean.
Continue reading ‘Multifactorial neural disruption in the brain of the Senegalese Sole (Solea senegalensis) under ocean acidification’Stressed overwintering bottleneck hypothesis: ocean warming and acidification synergistically disrupt Arctic zooplankton overwintering
Published 1 December 2025 Science ClosedTags: Arctic, biological response, crustaceans, laboratory, molecular biology, mortality, multiple factors, physiology, reproduction, respiration, temperature, zooplankton
Ocean warming (OW), driven by the influx of warm Atlantic water masses, and acidification (OA) are threatening Arctic marine ecosystems. However, their potential synergistic effects are poorly understood, especially during the Polar Night when marine species are particularly vulnerable to stressors. Here, we tested our novel Stressed Overwintering Bottleneck Hypothesis (SOBH): warming will disrupt the overwintering of the keystone pan-Arctic copepod Calanus glacialis, a pivotal secondary producer, by impairing fitness-related traits underpinning survival and reproduction. We exposed C. glacialis to current and projected future OW levels (0 °C and 4 °C) and OA levels (pH 8.0 and 7.4-7.3) for 53 days during the mid-Arctic Polar Night. We assessed survival, development, and physiological and molecular mechanisms (oxygen consumption, lipid depletion, the expression of nine targeted genes related to oxidative stress and damage repair, and DNA damage). OW alone did not affect C. glacialis mortality; however, OA increased copepod survival at 0 °C. Notably, their combined effects (OWA) synergistically doubled mortality, as predicted by SOBH. Warming also accelerated moulting from copepodite stage V to adulthood in December, and increased respiration, exhausted lipid reserves entirely by early March, approximately one to four months before the spring algal bloom, further supporting SOBH. DNA damage and gene expression patterns indicated low investment in maintenance and damage repair. Collectively, these findings reveal hidden mechanisms by which OW and OA synergistically threaten overwintering Calanus copepods by drastically increasing mortality, accelerating moulting, raising metabolic rates, and causing early lipid depletion. These effects generate cross-seasonal phenological mismatches among overwintering survival, energy reserves, reproduction, and primary production. Such stressed overwintering bottlenecks in foundational secondary producers like Calanus copepods provide novel explanations for how OW and OA can constrict Arctic marine food webs. At a broader perspective, SOBH highlights how multiple stressors induced overwintering disruption could reshape pan-Arctic and global biodiversity.
Continue reading ‘Stressed overwintering bottleneck hypothesis: ocean warming and acidification synergistically disrupt Arctic zooplankton overwintering’Physiological and transcriptomic responses of Sargassum hemiphyllum var. chinense to ocean acidification and nitrogen enrichment
Published 21 November 2025 Science ClosedTags: algae, biological response, laboratory, molecular biology, multiple factors, North Pacific, nutrients, physiology
Sargassum hemiphyllum var. chinense is a major brown macroalga and has important ecological and economic significance. Ocean acidification and nitrogen enrichment are serious threats to marine ecosystems primarily by altering the physiology of organisms. However, the response of S. hemiphyllum var. chinense to the combined effects of ocean acidification and elevated nitrogen levels remains unclear. This study conducted a 7-day dual-factor experiment to investigate the physiological and transcriptional responses of S. hemiphyllum var. chinense under two CO2 levels (400 μatm and 1000 μatm) and two NO3⁻ levels (50 μmol/L and 300 μmol/L). The results showed that high CO2 and NO3− concentrations promoted the synthesis of photosynthetic pigments including qN and NPQ. Physiological results showed that high CO2 and the combined high NO3− and CO2 treatments enhanced growth rate and NO3− uptake rate, but NR activity was significantly decreased. Transcriptome analysis identified differentially expressed genes involved in oxidative phosphorylation, carbon metabolism, the TCA cycle, and nitrogen metabolic pathways. Notably, genes related to oxidative phosphorylation and TCA cycle were significantly up-regulated under high NO3− and dual-factor treatments, suggesting that carbohydrate metabolism and energy metabolism of S. hemiphyllum var. chinense were significantly enhanced. The qRT-PCR analysis revealed that the expression levels of key genes involved in carbon fixation and nitrogen metabolism, including PFK, PRK, GAPDH, Rubisco, NR, and MDH, were significantly downregulated. These findings elucidate the molecular mechanisms by which S. hemiphyllum var. chinense adapts to ocean acidification and nitrogen enrichment, offering valuable insights for understanding its capacity to withstand changing marine environments.
Continue reading ‘Physiological and transcriptomic responses of Sargassum hemiphyllum var. chinense to ocean acidification and nitrogen enrichment’Impact of ocean acidification on the intestinal microflora of Sinonovacula constricta
Published 20 November 2025 Science ClosedTags: biological response, BRcommunity, community composition, laboratory, molecular biology, mollusks, North Pacific, otherprocess, prokaryotes
The intestinal microflora, which is vital for nutrient absorption and immune regulation, can experience dysbiosis under environmental stress, potentially enhancing host susceptibility to pathogenic invasion. The impact of ocean acidification on bivalves is substantial, but its effects on their intestinal microflora remain poorly understood. To explore the impact of ocean acidification on the intestinal microflora of Sinonovacula constricta, this study used high-throughput 16S rRNA sequencing technology to investigate the variations in the intestinal microflora communities of S. constricta during ocean acidification across different time points. After exposure to ocean acidification, changes in the composition of the intestinal microflora of S. constricta were observed, with no significant difference in α-diversity between the acidified and control groups. The abundance of Proteobacteria in the acidification group increased, whereas that of Cyanobacteria decreased. The abundance of Firmicutes initially decreased and then increased. At the genus level, the relative abundance of Pseudomonas was lower than that in the control group, whereas the relative abundance of Photobacterium, Acinetobacter, and Enterobacter gradually increased. LEfSe analysis identified Serpens as the discriminative biomarker at 7 days of acidification, Enterobacteriales, Rhodobacteraceae, and Martvita at 14 days of acidification, and Serpens, Acidibacteria, and Aeromonadaceae at 35 days of acidification. Functional prediction analysis indicated significant stimulation in various metabolic pathways at different time points following acidification stress. Specifically, pathways involved in biosynthesis were significantly stimulated at 14 days of acidification, while those related to sucrose degradation were disrupted at 35 days. The results further indicated that ocean acidification stress can influence the intestinal microflora of S. constricta, but no severe dysbiosis or digestive system impairment was observed at the microbial level. This study provides new insights into the effects of ocean acidification on the intestinal microflora of marine bivalves.
Continue reading ‘Impact of ocean acidification on the intestinal microflora of Sinonovacula constricta’Integrative analysis of coral plasticity and adaptations reveals key proteins driving resilience to changes in ocean carbonate chemistry
Published 14 November 2025 Science ClosedTags: adaptation, biological response, calcification, corals, laboratory, molecular biology, otherprocess, physiology
Understanding how corals adapt to changes in seawater carbonate chemistry is crucial for developing effective coral conservation strategies. Research to date has mostly focused on short-term experiments, overlooking long-term evolutionary effects. Here, we investigated the link between short-term stress responses and long-term genetic adaptations in the coral species Porites pukoensis through experiments under varying CO2 and alkalinity conditions. Our results showed that alkalinity enrichment significantly increased coral calcification rates by 35%-45% compared to high CO2 treatment, highlighting the potential of alkalinity enrichment to mitigate acidification impacts. Corals modulated relative expression levels of basic and acidic proteins in response to changes in seawater carbonate chemistry in the stress experiments. Genomic data revealed that this mechanism has been evolutionarily fixed in various organisms adapting to seawater carbonate chemistry. Additionally, both experimental and genomic results showed that extracellular matrix proteins, like collagen with von Willebrand factor type A domain, were modified in response to distinct carbonate environments. Molecular dynamics simulations and in-vitro experiments demonstrated that the structural stability of these proteins contributes to coral resilience under acidified conditions. This study established an integrated framework combining stress experiments, multi-omics analyses, molecular simulations, and in-vitro validation to identify key proteins involved in coral adaptation to acidification.
Continue reading ‘Integrative analysis of coral plasticity and adaptations reveals key proteins driving resilience to changes in ocean carbonate chemistry’Mothers know best: maternal signaling boosts larval resilience under ocean acidification conditions
Published 12 November 2025 Science ClosedTags: adaptation, biological response, fisheries, molecular biology, mollusks, morphology, mortality, otherprocess, physiology, reproduction
Highlights
- Environmental priming effectively rescued larval phenotype under OA conditions.
- Egg ‘omics were investigated to elucidate mechanism of priming across generations.
- Clam egg lipidomes were largely unperturbed by maternal low-pH exposure.
- Differentially expressed genes were identified in eggs of low-pH primed clams.
Abstract
Bivalve aquaculture is a growing sector worldwide, producing sustainable animal protein to meet growing demand from consumers. Yet, the industry remains vulnerable to environmental changes that can impact their product across life stages, especially at the larval stage. Parental priming, or the exposure of broodstock to adverse environmental conditions as they undergo gametogenesis, holds promise as a method to increase resilience in bivalve offspring. We exposed Manila clam (Ruditapes philippinarum) broodstock to low pH conditions (pH 7.4 for 78 days during gametogenesis). Larvae were produced from primed (low pH) and unprimed (ambient pH) broodstock and exposed to ambient or low pH conditions in a full factorial design. Larval phenotype in response to low pH was partially rescued by broodstock priming: larvae from low pH-exposed broodstock had better survival and growth than larvae from broodstock held under ambient conditions. Clam egg lipidomic and transcriptomic analyses were performed to determine the physiological differences associated with broodstock environmental conditions. Egg lipid abundance profiles were not significantly different between parental treatments. The egg transcriptome revealed 48 differentially expressed transcripts associated with parental environmental conditions. These genes are involved in important processes for early larval physiology, including metabolism, cell cycle, and transcriptional regulation. Broodstock clams were minimally impacted by their exposure to low pH for 78 days, however we show here that subtle maternal signals may contribute to the vastly improved larval performance observed under low pH conditions.
Continue reading ‘Mothers know best: maternal signaling boosts larval resilience under ocean acidification conditions’Transcriptomic analysis of the hepatopancreas response to low-pH stress in kuruma shrimp (Marsupenaeus japonicus)
Published 6 November 2025 Science ClosedTags: biological response, crustaceans, fisheries, laboratory, molecular biology, North Pacific, physiology
Highlights
- Low-pH stress disrupted oxidative balance in M. japonicus, suppressing SOD and CAT activities while increasing MDA levels.
- Low-pH stress triggered 2705 DEGs in hepatopancreas linked to immunity, oxidative stress, and energy metabolism.
- CTSD, GLB1, and LGI4 are implicated in long-term immune adaptation to low pH.
- Key pathways—lysosome, Toll-like receptor, AMPK, and PPAR signaling—were activated under low pH stress.
- Hub genes such as NADH-GOGAT and MDHM were identified as central regulators of antioxidant defense and energy metabolism.
Abstract
Ocean acidification has emerged as a globally recognized environmental issue, posing a serious threat to marine ecosystems. To elucidate the adaptive mechanisms of Marsupenaeus japonicus under acidified conditions, both biochemical and transcriptomic analyses were performed following low-pH exposure. Biochemical assays revealed that low pH stress significantly SOD and CAT activities while markedly elevating MDA levels, indicating oxidative damage. T-AOC exhibited a transient rise followed by a sharp decline at later stages, suggesting initial activation and subsequent exhaustion of antioxidant defense. Transcriptomic profiling identified 2705 DEGs that were primarily enriched in pathways related to immune regulation, redox balance, apoptosis, and energy metabolism, including the lysosome, Toll-like receptor, and PPAR signaling pathways. Protein interaction analysis identified 9 hub genes, including NADH-GOGAT and MDHM, which may play key roles in antioxidant defense and metabolic regulation. The integration of enzyme activity and transcriptomic data indicates that acid stress initially induces oxidative imbalance, followed by compensatory activation of antioxidant and immune systems to restore cellular homeostasis. These findings provide comprehensive insights into the oxidative stress adaptation of M. japonicus and offer a genetic and physiological foundation for breeding acid-tolerant shrimp strains.
Continue reading ‘Transcriptomic analysis of the hepatopancreas response to low-pH stress in kuruma shrimp (Marsupenaeus japonicus)’Omics insights into ocean health: molecular adaptations and ecosystem resilience under climate stress
Published 5 November 2025 Science ClosedTags: biological response, molecular biology, policy, review
Despite extensive research documenting the impacts of climate change on marine ecosystems, the molecular mechanisms driving organismal and ecosystem resilience to ocean warming, acidification, and deoxygenation remain insufficiently understood. This review addresses this knowledge gap by synthesizing recent advances in omics technologies—including genomics, transcriptomics, proteomics, metabolomics, and epigenomics—that illuminate adaptive genetic, metabolic, and epigenetic processes in marine organisms. These approaches help identify climate-tolerant genetic variants, uncover metabolic pathways for stress mitigation, and reveal epigenetic modifications enabling rapid adaptation. Together, such insights are transforming biodiversity monitoring, predictive ecosystem modeling, and the evidence-based design of climate-resilient marine protected areas (MPAs) grounded in genomic and functional diversity. Studies on marine microbial communities further provide promising avenues for blue carbon ecosystem enhancement and climate mitigation. Integrating omics findings into global governance frameworks, including the United Nations Convention on the Law of the Sea (UNCLOS) and International Maritime Organization (IMO), strengthens adaptive fisheries management, spatial planning, and climate-resilient policy. Key challenges for multi-omics integration are discussed alongside innovative solutions, such as integrative analytical approaches and the adoption of standardized molecular indicators. By bridging molecular science, policy, and management, this review outlines how interdisciplinary collaboration can advance adaptive and sustainable stewardship of the ocean in an era of unprecedented environmental change.
Continue reading ‘Omics insights into ocean health: molecular adaptations and ecosystem resilience under climate stress’The negative responses and acclimation mechanisms of Neopyropia yezoensis conchocelis filaments to short- and long-term ocean acidification
Published 30 October 2025 Science ClosedTags: adaptation, algae, biological response, growth, laboratory, molecular biology, North Pacific, otherprocess, photosynthesis, physiology
Background
Ocean acidification (OA) significantly alters the carbonate chemistry of seawater, leading to a decrease of seawater pH to impact the physiological and biochemical processes of those intertidal macroalgae. Previous studies have focused on the response of macroalgae to OA at thallus stage, while the effects at filamentous stage remain insufficiently explored.
Results
This study investigated the physiological-biochemical and molecular mechanisms of the filamentous conchocelis stage (the diploid sporophyte) of Neopyropia yezoensis responding to short- (5 days) and long-term (20 days) OA (2000 ppm CO2, pH 7.53). The results showed that short-term OA rapidly inhibited the growth and photosynthesis, suppressed chlorophyll synthesis and nitrogen assimilation, and down-regulated genes associated with photosynthesis, Calvin cycle, and carbohydrate metabolism of N. yezoensis conchocelis filaments. However, N. yezoensis conchocelis filaments showed acclimation strategies under long-term OA, in terms of metabolic reorganization, prioritizing stress tolerance over growth. Further weighted gene co-expression network analysis (WGCNA) based on the metabolomic and transcriptomic results under long-term OA showed that the strategy was manifested by the accumulation of soluble sugars as osmolytes, lipid β-oxidation compensating for energy deficits, and H+ extrusion mediated via ABC transporters.
Conclusions
This study suggested time-depended responses of N. yezoensis conchocelis filaments to OA, proving the pronounced negative effects of OA on N. yezoensis conchocelis filaments, revealing N. yezoensis conchocelis filaments could acclimate to long-term OA by resource reallocation. These findings provide new insight into the survival of N. yezoensis conchocelis filaments under OA, and facilitate the development of technologies and breeding strategies for improved acidification tolerance in N. yezoensis.
Continue reading ‘The negative responses and acclimation mechanisms of Neopyropia yezoensis conchocelis filaments to short- and long-term ocean acidification’Ocean acidification enhances TiO2 nanoparticle toxicity in Oryzias melastigma: dominant role of size effects in driving bioaccumulation and hepatotoxicity
Published 21 October 2025 Science ClosedTags: biological response, fish, laboratory, molecular biology, multiple factors, physiology, toxicants
Highlights
- OA reduces TiO₂ NPs aggregation/sedimentation, increasing NP bioaccumulation
- NPs preferentially accumulate in liver, inducing hepatotoxicity via oxidative stress
- Size effect outweighs biological resistance as primary NP toxicity driver under OA
- Combined OA-NPs suppress hepatic genes, activate senescence and cell death pathways
- First evidence quantifying hydrodynamic size dominance in OA-enhanced NP toxicity
ABSTRACT
Ocean acidification (OA) and engineered nanoparticles (NPs) pollution represent two critical global environmental challenges. Marine organisms are suffering from their combined stress. However, few studies address their combined effects, and the toxicity mechanisms of NPs under OA are largely unresolved. In this study, we investigated the responses of the marine medaka Oryzias melastigma to environmentally relevant concentration of TiO2 NPs (1.0 mg/L) under OA (pH 7.40). We found that OA alleviated the aggregation and sedimentation of NPs, and decreased the resistance ability of the marine medaka to NPs stress, leading to elevated bioaccumulation of TiO2 NPs. Notably, NPs preferentially accumulated in the liver, inducing hepatotoxicity through oxidative stress and histopathological and ultrastructural damage. Critically, an integrated biomarker approach quantified the relative contributions of size effects (58%) and biological resistance (42%) to NP toxicity under OA, demonstrating that hydrodynamic size dominates toxicity outcomes. Transcriptomic analysis further revealed suppressed hepatic gene transcription and translation, alongside activated cellular senescence and programmed cell death pathways under combined exposure. These findings provide critical insight into the combined toxicity mechanisms of NPs and OA, significantly advancing our understanding of the profound risks that NPs pose to marine ecosystems under OA conditions.
Continue reading ‘Ocean acidification enhances TiO2 nanoparticle toxicity in Oryzias melastigma: dominant role of size effects in driving bioaccumulation and hepatotoxicity’Dulse seaweed Devaleraea mollis mitigates effects of ocean acidification on larval Pacific oysters Magallana gigas
Published 21 October 2025 Science ClosedTags: algae, biological response, BRcommunity, chemistry, laboratory, mitigation, molecular biology, mollusks, morphology, North Pacific, reproduction
Ocean acidification (OA), driven by upwelling and climate change, can negatively impact the ecological and economic contribution of marine calcifiers along coasts worldwide. OA interferes with calcification, particularly in early life stages, causing mortality, reduced growth, and morphological abnormalities in shellfish such as the Pacific oyster (Magallana gigas). This issue is gaining traction as climate change intensifies, placing shellfish in wild populations and farms alike at risk. Macroalgal photosynthesis by seaweed such as Pacific dulse (Devaleraea mollis) has been proposed to provide small-scale OA refuges, but few controlled experiments quantify this effect, and none have focused on larval shellfish. This study examines the potential for Pacific dulse to mitigate OA and its effects on Pacific oyster larvae. Under continuous light for 23 days, the presence of dulse resulted in a consistent increase in seawater aragonite saturation state by 0.1-0.9, and pH by 0.1-0.5 units, depending on OA condition. Newly fertilized oysters were reared for 48 hours in the absence or presence of dulse under treatments corresponding to ambient (pH 7.8, 450 μatm CO₂), future OA (pH 7.6, 800 μatm CO₂), and future OA + upwelling (pH 7.4, 1200 μatm CO₂) seawater conditions. Dulse fully mitigated OA effects on larval size that ranged from decreases of 5% to 10%. Under the future OA + upwelling treatment, dulse presence reduced the odds of underdeveloped oyster larvae at 14 hours post fertilization (hpf), and larvae with hinge abnormalities at 24 hpf, by over 50%. Dulse induced minor changes to immune response gene expression at 48 hpf. These findings highlight the benefits of seaweed when adjacent to organisms sensitive to OA. These findings will be particularly useful for shellfish farms, habitat restoration efforts, and ocean stewardship practices as a potential mitigation strategy under the changing climate.
Continue reading ‘Dulse seaweed Devaleraea mollis mitigates effects of ocean acidification on larval Pacific oysters Magallana gigas’DNA methylation plasticity drives copepod resilience to coastal high pCO2 and cadmium pollution under multigenerational exposure
Published 20 October 2025 Science ClosedTags: adaptation, biological response, crustaceans, laboratory, metals, molecular biology, mortality, multiple factors, North Pacific, otherprocess, reproduction, zooplankton
Highlights
- Fluctuating acidification caused the most Cd multigenerational toxicity in copepods.
- The adverse effects of acidification and Cd tended to intensify during F1-F3.
- The copepods potentially adapted to combined exposure in F4.
- DNA hypomethylation rendered copepods presenting the adaptive potential.
ABSTRACT
The vast majority of coastal organisms have been facing multigenerational scenarios of fluctuatingly high pCO2 and Cd pollution in their natural habitats. However, the adaptive capacity of these organisms to such combined stressors and the underlying mechanisms remain poorly understood. In this study, we conducted a multigenerational experiment (F1-F4) to investigate the adaptive responses of the marine copepod Tigriopus japonicus to combined fluctuatingly high pCO2 and Cd exposure, along with the associated mechanisms. Our findings revealed that steady high pCO2 aggravated Cd multigenerational toxicity, and it was more under fluctuating acidification. Notably, by the F4 generation, copepods potentially adapted to the combined stressors. Through transcriptomic and DNA methylation analyses of copepods from the F1 and F4 generations, we found that under combined exposure, F1 copepods likely reallocated more energy to counteract Cd toxicity; however, DNA hypermethylation inhibited Cd exclusion and detoxification/stress response pathways, ultimately compromising development and reproduction. In contrast, in the F4 generation, DNA hypomethylation enhanced processes such as cuticle repair program, compensatory mechanism (e.g., detoxification and immune response), and reproduction, consequently increasing the copepod’s fitness. These findings reveal an epigenetic basis for phenotypic acclimatization, offering marine copepods a supplementary mechanism to cope with combined stressors.
Continue reading ‘DNA methylation plasticity drives copepod resilience to coastal high pCO2 and cadmium pollution under multigenerational exposure’
