Marine habitat-forming species provide crucial ecosystem functions and services worldwide. Still, the individual and combined long-term effects of ocean acidification and warming on bryozoan populations, structures, and microbiomes remain unexplored. Here, we investigate the skeletal properties, microbiome shifts, and population trends of two bryozoan species living inside and outside a volcanic CO2 vent, a natural analog to future ocean acidification conditions. We show that bryozoans can acclimatize to acidification by adjusting skeletal properties and maintaining stable microbiomes. However, we document a decrease in microbial genera playing essential functions under acidified conditions. Moreover, we show that ocean acidification exacerbates bryozoan cover loss and mortality caused by ocean warming. The observed shifts in the microbiome and cover suggest that, despite their morphological plasticity, bryozoan species will be heavily impacted by future ocean conditions, posing a threat to many benthic ecosystems in which they play a pivotal role.
Continue reading ‘Interactive effects of ocean acidification and warming disrupt calcification and microbiome composition in bryozoans’Posts Tagged 'molecular biology'
Interactive effects of ocean acidification and warming disrupt calcification and microbiome composition in bryozoans
Published 12 August 2025 Science ClosedTags: abundance, adaptation, biological response, BRcommunity, bryozoa, community composition, communitymodeling, field, Mediterranean, modeling, molecular biology, morphology, mortality, otherprocess, prokaryotes, vents
Identification, characterization, and expression analysis reveal regulatory roles of MCM genes in Patinopecten yessoensis under low-pH stress
Published 12 August 2025 Science ClosedTags: adaptation, biological response, laboratory, molecular biology, mollusks, North Pacific, otherprocess, reproduction
Highlights
- Nine MCM genes are systematically identified from Patinopecten yessoensis genome.
- PyMCMs are widely expressed during development and adult tissues, especially PyMCM6.
- PyMCM5 is particularly sensitive to low pH stress, whereas PyMCM8 and PyMCM9 are not.
- Scallops reduce DNA replication but maintain DNA repair in response to low-pH stress.
Abstract
The Yesso scallop (Patinopecten yessoensis), an ecomically important bivalve species, exhibits high susceptibility to ocean acidification. The growth retardation induced by low-pH stress poses a significant challenge for Yesso scallop aquaculture. However, the molecular mechanisms underlying this phenomenon are not well understood. Considering the pivotal role of cell proliferation in organism growth, we investigated the minichromosome maintenance (MCM) family in P. yessoensis, which are key regulators of DNA replication initiation and cell cycle regulation. In this study, we identified nine MCM genes (PyMCM2–10) in the P. yessoensis genome. These PyMCMs exhibit highly conserved sequence characteristics and typical MCM domains. Phylogenetic analysis showed that PyMCMs cluster into nine distinct clades, underscoring their strong evolutionary conservation across species homologs. Spatiotemporal expression profiling demonstrated widespread expressions of PyMCMs throughout all developmental stages and adult tissues, with particularly high levels in vigorous cell proliferation (e.g., up to 318 TPM in multicell stage and up to 202 TPM in gonad tissue). Notably, PyMCM6 exhibited consistently high expression across development and across tissues (> 44 TPM), suggesting a key regulatory role in both development and tissue maintenance. Under low-pH stress, the expressions of PyMCMs were downregulated to varying degrees, with PyMCM5 showing the most significant reduction (|log2FC| up to 3.5), while PyMCM8 and PyMCM9 remained relatively stable. This pattern suggests a strategic response that scallops reduce DNA replication capacity (mediated by PyMCM2–7) but potentially maintain DNA repair functions (associated with PyMCM8/9 stability) to mitigate damage induced by low-pH, potentially explaining the intrinsic inhibition of cell proliferation. Quantitative real-time PCR and in situ hybridization further confirmed that low-pH stress inhibits PyMCMs expressions (p < 0.05), with the effect amplified as pH decreases. Collectively, these findings enhance our understanding of PyMCMs in regulating bivalve growth retardation under low-pH stress and provide valuable insights into the mechanisms of environmental adaptation in bivalves.
Continue reading ‘Identification, characterization, and expression analysis reveal regulatory roles of MCM genes in Patinopecten yessoensis under low-pH stress’Skeleton-forming responses of reef-building corals under ocean acidification
Published 7 August 2025 Science ClosedTags: biological response, corals, laboratory, molecular biology, morphology, North Pacific
Ocean acidification is becoming more prevalent and may contribute to coral reef degradation, yet our understanding of its role in global reef decline remains limited. Therefore, there is an urgent need to study the impact of reduced pH levels on the growth patterns of major reef-building corals. Here, we studied the skeleton-forming strategies of 4 widely distributed coral species in a simulated acidified habitat with a pH of 7.6 to 7.8. We reconstructed and visualized the skeleton-forming process, quantified elemental calcium loss, and determined gene expression changes. The results suggest that different reef-building corals have diverse growing strategies in lower pH conditions. A unique “cavity-like” forming process starts from the inside of the skeletons of Acropora muricata, which sacrifices skeletal density to protect its polyp–canal system. The forming patterns in Pocillopora damicornis, Montipora capricornis, and Montipora foliosa were characterized by “osteoporosis”, exhibiting disordered skeletal structures, insufficient synthesis of adhesion proteins, and low bone mass, correspondingly. In addition, we found that damage from acidification particularly affects pre-existing skeletal structures in the colony. These results enhance our understanding of skeleton-forming strategies in major coral species under lower pH conditions, providing a foundation for coral reef protection and restoration amidst increasing ocean acidification.
Continue reading ‘Skeleton-forming responses of reef-building corals under ocean acidification’Impact of CO2-induced aquatic acidification on environmental DNA and RNA shedding and persistence
Published 5 August 2025 Science ClosedTags: biological response, laboratory, mesocosms, molecular biology, mollusks
Anticipated future increases in CO2 levels are predicted to have a diverse array of lethal and non-lethal effects on the marine ecosystem. While there has been extensive research on the physiological impacts of ocean acidification on marine species, our understanding of how increasing levels of carbon dioxide affect the shedding and decay of environmental DNA and RNA (eDNA/ eRNA) in marine habitats is limited. This may impede the effective adoption of environmental nucleic acid–based molecular tools for monitoring marine biodiversity and detecting rare or invasive species. In the present study, we conducted mesocosm experiments to determine the shedding and decay rate constants of eDNA and eRNA in M. gigas (Magallana [Crassostrea] gigas) using mitochondrially encoded tRNA leucine 1 (mt-tl1) marker at various partial pressures of CO2 in seawater. To our knowledge, this is the first study manipulating seawater pH using CO2. We developed a sensitive and specific quantitative PCR-based assay to detect M. gigas eDNA and eRNA. Higher CO2 levels increased shedding rates, indicating greater organism stress and biological effects on oysters. Additionally, increased CO2 accelerates DNA and RNA decay, suggesting that ocean acidification may impact the reliability of eDNA-based biodiversity monitoring. Furthermore, eRNA displayed lower steady-state concentrations and a shorter persistence time in comparison to eDNA, as is consistent with known biochemical properties of the molecules. These findings are presented in the context of previous work that adjusted pH through acid–base adjustment and temperature and highlight the importance of considering ocean acidification caused by differing CO2 levels when using molecular tools for marine conservation and fisheries management.
Continue reading ‘Impact of CO2-induced aquatic acidification on environmental DNA and RNA shedding and persistence’Epigenetic insights into physiological resilience: multigenerational readouts of CO2-induced seawater acidification effects on fish embryos
Published 5 August 2025 Science ClosedTags: adaptation, biological response, fish, laboratory, molecular biology, morphology, otherprocess, physiology, reproduction
Highlights
- Ocean acidification causes generation-specific developmental and metabolic changes.
- F2 embryos show enhanced resilience through transcriptional recovery mechanisms.
- Hypomethylation of ion transport genes drives adaptive acid-base regulation.
- Epigenetic inheritance facilitates multigenerational acclimation to acidification.
Summary
Anthropogenic CO2 emissions are acidifying oceans, threatening marine organisms during early development. We investigated multigenerational effects of projected 2100 acidification (pH 7.6) on marine medaka (Oryzias melastigma) embryos across three generations using integrated phenotypic, physiological, transcriptomic, and epigenetic analyses. Prolonged acidification altered developmental trajectories, with F2 embryos showing size reductions. Metabolic responses were generation-specific: F0 embryos displayed decreased ammonium excretion, while F1 and F2 maintained stable profiles. Transcriptomic analysis revealed generational changes in neurotransmission, ion regulation, and epigenetic pathways. F2 embryos exhibited attenuated transcriptional perturbations and partial restoration of acid-base homeostasis, suggesting enhanced adaptability. Adaptive gene expression correlated with hypomethylation recovery of ion transport genes AE1a and NHE2 in F2 embryos. Increased hypomethylated AE1a promoter CpG sites in F1 and F2 generations aligned with elevated transcription, indicating epigenetically-driven enhancement. These results demonstrate epigenetic control’s crucial role in multigenerational plasticity and adaptive responses to ocean acidification.
Continue reading ‘Epigenetic insights into physiological resilience: multigenerational readouts of CO2-induced seawater acidification effects on fish embryos’Complementary genetic and epigenetic changes facilitate rapid adaptation to multiple global change stressors
Published 1 August 2025 Science ClosedTags: adaptation, biological response, crustaceans, laboratory, molecular biology, multiple factors, otherprocess, temperature, zooplankton
Significance
Organisms must adapt or acclimate to survive global change, but how these processes interact and the role of epigenetic variation is unknown. We experimentally evolved the marine copepod Acartia tonsa for 25 generations in global change conditions and measured their genomic, epigenomic, and gene expression responses. We found that both genetic and epigenetic changes contributed to resilience and were inversely related, acting in different regions of the genome. Epigenetic changes were functionally linked to the regulation of stress and transposable elements and correlated with shifts in gene expression. These findings paint a surprising picture of the complementary contributions of both genetic and epigenetic mechanisms to population resilience in global change conditions.
Abstract
To persist under unprecedented rates of global change, populations can adapt or acclimate. However, how these resilience mechanisms interact, particularly the role of epigenetic variation in long-term adaptation, is unknown. To address this gap, we experimentally evolved the foundational marine copepod Acartia tonsa for 25 generations under ocean acidification, warming, and their combination and then measured epigenomic, genomic, and transcriptomic responses. We observed clear and consistent epigenomic and genomic divergence between treatments, with epigenomic divergence concentrated in genes related to stress response and the regulation of transposable elements. However, epigenetic and genetic changes were inversely related and occurred in different regions of the genome; levels of genetic differentiation (FST) were up to 2.5× higher in regions where methylation did not differ between treatments compared to regions with significant methylation changes. This negative relationship between epigenetic and genetic divergence could be driven by local inhibition of one another or distinct functional targets of selection. Finally, epigenetic divergence was positively, though weakly, associated with gene expression divergence, suggesting that epigenetic changes may facilitate phenotypic change. Taken together, these results suggest that unique, complementary genetic and epigenetic mechanisms promote resilience to global change.
Continue reading ‘Complementary genetic and epigenetic changes facilitate rapid adaptation to multiple global change stressors’Impacts of multiple coastal stressors across life-history stages in the eastern oyster
Published 31 July 2025 Science ClosedTags: adaptation, biological response, laboratory, molecular biology, mollusks, multiple factors, otherprocess, oxygen, reproduction
Urbanized estuaries are characterized as a complex of biotic and abiotic stressors, which currently challenge marine life and are expected to intensify and become increasingly unpredictable under the ongoing impacts of climate change. The persistence of coastal species that inhabit these stressful environments will ultimately depend on their ability to adapt. Many of these species have complex life cycles, featuring distinct morphological and physiological developmental stages that can exhibit unique responses to environmental pressures. However, since all stages share the same genome, selective pressures acting on one stage can have cascading effects throughout the life cycle. The larval stage, being particularly sensitive to environmental stressors and often the only free-moving stage, plays a crucial role in gene flow across populations. Consequently, selection during this stage can set the trajectory for the entire life cycle and significantly influence the adaptive structure of populations. This dissertation explores the impacts of multiple environmental stressors across the life-history stages of the eastern oyster (Crassostrea virginica). In Chapter 1, we integrated genomic information about larval stressor response into a seascape genomics framework, using adult oysters sampled from various localities with differing environmental profiles in Narragansett Bay, Rhode Island. We identified environmentally driven signatures of local adaptation corresponding to different genomic regions, even amidst high gene flow. In loci putatively under selection in larvae exposed to coastal stressors, we found stressor-specific associations with environmental conditions that aligned with adult candidate loci, highlighting the critical role of the larval stage in shaping population adaptive divergence. In Chapter 2, we exposed genetically diverse pools of larval oysters to diurnal fluctuating acidification and hypoxia for most of their development. Genomic analysis of samples taken before and after exposure revealed substantial shifts in allele frequencies at loci putatively under selection, suggesting a potential for rapid adaptation to future environmental conditions. Chapter 3 extended this work by exposing oysters to these stressors from the pediveliger stage, through settlement, and into early juvenile development. Genomic analysis from the larval and settlement exposure periods revealed both unique and shared signatures of selection across the early developmental stages. While the juvenile stage was more tolerant to the stressor conditions, we found that stressor exposure through the pediveliger larval and settlement stages had short-term carryover effects on juvenile performance. These findings demonstrate the complex connection of evolutionary responses across the full life cycle. While early developmental stages are sensitive to coastal stressors, our analysis reveals adaptive responses that highlight the resilience of this species. Specifically, these early life-stage responses can influence later developmental stages, shaping the species’ overall adaptive capacity and impacting population structure dynamics. Consequently, understanding these dynamics is crucial for predicting how population structure and adaptive divergence will evolve in response to intensifying coastal stressors.
Continue reading ‘Impacts of multiple coastal stressors across life-history stages in the eastern oyster’Adaptive responses of large yellow croaker Larimichthys crocea to ocean acidification: integrative analysis of gill and kidney transcriptomics and antioxidant enzyme activities
Published 21 July 2025 Science ClosedTags: adaptation, biological response, fish, laboratory, molecular biology, morphology, North Pacific, otherprocess, physiology
Anthropogenic acidification is a long-term challenge to marine ecosystems. Though coastal acidification is intensifying, the large yellow croaker (Larimichthys crocea) exhibits good adaptability to pH fluctuations, the underlying mechanisms of which remain poorly understood. This study investigated the morphology, antioxidant enzyme activity, and gene expression of L. crocea under varying acidification conditions (pH 8.1 (H group), 7.8 (M group), and 7.4 (L group)). Water pH fluctuations were also monitored to explore the physiological responses and potential adaptive molecular mechanisms of L. crocea under various acidified environments. The results indicated that the water pH decreased in the H group, significantly increased in the L group (p < 0.05), and remained stable in the M group during the experiment. The lowest MDA content and the highest antioxidant enzyme activities (CAT, SOD, GSH-Px) were observed in L. crocea at pH 7.8, suggesting pH 7.8 was optimal for L. crocea. Transcriptomic analysis revealed distinct gene expression patterns between the gills and kidneys under acidification stress. Differentially expressed genes (DEGs) in the gills were primarily observed between the M and L groups (62.3%), whereas in the kidneys, the majority of DEGs were observed between the M and H groups (43.2%). These findings suggested that the gills play a critical role in adapting to low pH in L. crocea, while the kidneys were more responsive to high pH. Enrichment analysis identified critical pathways, including vasopressin-regulated water reabsorption, mineral reabsorption, and aldosterone-regulated sodium reabsorption, which are associated with water and ion metabolism. These pathways play a pivotal role in the acid–base homeostasis and metabolism of L. crocea. These results provide insights into the adaptive mechanisms of L. crocea to acidified environments, with implications for aquaculture management and future ocean acidification adaptation.
Continue reading ‘Adaptive responses of large yellow croaker Larimichthys crocea to ocean acidification: integrative analysis of gill and kidney transcriptomics and antioxidant enzyme activities’High sensitivity to ocean acidification in wild out-migrating juvenile Pacific salmon is not impacted by feeding success
Published 18 July 2025 Science ClosedTags: biological response, fish, laboratory, molecular biology, mortality, multiple factors, North Pacific, physiology, reproduction
Salmon populations are declining worldwide, with high mortality rates during juvenile marine migration presenting a bottleneck to recruitment. The ocean conditions along the main migratory route of juvenile salmon in British Columbia are characterized by high variability in CO2, with the amplitude, duration, and frequency of ocean acidification events exacerbated by climate change. Similarly, the variability in ocean conditions affects the abundance and diversity of plankton prey, leading to areas of food paucity for juvenile salmon. We investigated the combined effects of ocean acidification (control and 3200 μatm CO2) and food limitation (ad libitum, ½ ration, and food deprived) on the survival, condition, and gene expression profiles of juvenile Chum salmon (Oncorhynchus keta) to develop predictive biomarkers for CO2 exposure and food deprivation. Ocean acidification caused a direct 3-fold increase in mortality over 25 days of exposure, which was unaffected by food availability but differentially affected smaller fish. CO2 exposure induced transcriptomic changes in a suite of genes associated with ion regulation, while food deprivation was associated with a differential expression of stress, immune, and mortality markers, as well as reduced condition factor. Our data indicate that CO2 directly impairs ionoregulatory capacity to the point of failure in juvenile Chum salmon and that these effects cannot be compensated through increased energy from food. Applying our gene panels as biomarkers to a subset of fish with known exposure, we were able to accurately predict exposure to CO2 and food deprivation (74% and 90%, respectively). By combining these gene panels with previously established biomarkers for other environmental stressors, the recent environmental stress history of wild fish can be determined and can be used in models to predict salmon returns, informing fisheries management and conservation efforts.
Continue reading ‘High sensitivity to ocean acidification in wild out-migrating juvenile Pacific salmon is not impacted by feeding success’Cross-generational plasticity in Atlantic silversides (Menidia menidia) under the combined effects of hypoxia and acidification
Published 17 July 2025 Science ClosedTags: biological response, fish, laboratory, molecular biology, mortality, multiple factors, North Atlantic, oxygen, physiology, reproduction
We investigated the potential for cross-generational plasticity to influence how offspring respond to hypoxia and ocean acidification (hereafter HypOA) in the coastal forage fish Atlantic silverside (Menidia menidia). Mature wild silversides were treated with a control (dissolved oxygen (DO):100% air saturation (a.s.) / pCO2: 650 µatm) or HypOA conditions (DO: 40% a.s. / pCO2: 2300 µatm) for 10 days prior to spawning. Their offspring were reared under both treatments in factorial experimental design. Parental environment had minimal effects on offspring phenotype: exposure to HypOA reduced survival and developmental rates regardless of parental treatment. However, RNAseq analysis revealed that direct offspring exposure to HypOA induced substantial transcriptional changes, with 1,606 differentially expressed transcripts (DETs) in larvae from control parents. These changes affected neural development, synaptic signaling, oxygen acquisition, and extracellular matrix organization. In contrast, larvae from HypOA-exposed parents exhibited a muted transcriptional response to HypOA, with only 4 DETs. Although we did not detect a statistically significant interaction between parental and offspring environments at the gene-wise level, a gene set test supported a consistent attenuation of expression changes in offspring from HypOA-treated parents. This pattern may be consistent with transcriptional frontloading, when stress-induced changes are retained and may modify future responses. However, because this effect did not improve offspring performance under HypOA, they are unlikely to represent an adaptive response. Instead, they may reflect non-adaptive carryover effects of parental exposure. Our findings highlight the potential for cross-generational effects to shape transcriptional plasticity, even in the absence of benefits to offspring.
Continue reading ‘Cross-generational plasticity in Atlantic silversides (Menidia menidia) under the combined effects of hypoxia and acidification’Combined effects of ocean acidification and warming on phytoplankton productivity and community structure in the coastal water of Southern East
Published 17 July 2025 Science ClosedTags: biological response, community composition, laboratory, mesocosms, molecular biology, multiple factors, North Pacific, otherprocess, photosynthesis, physiology, phytoplankton, temperature
Highlights
- Ocean warming partly offsets acidification-driven impacts on primary productivity in a southern coastal water of China.
- Acidification alters phytoplankton communities with increased proportions of dinoflagellates and reduced that of diatoms.
- Combination of warming and acidification reduced overall microbial diversity in the coastal water.
Abstract
Progressive global ocean changes, including ocean acidification and warming, are expected to impact ecosystems differentially due to regional environmental differences that govern biogeochemical and ecological processes. In this study, we investigated the impacts of ocean acidification and warming on the phytoplankton community and primary productivity in the southern coastal water of the East China Sea by running land-based mesocosms controlled under current atmospheric pCO2 (∼430 μatm) and projected levels for the year 2100 (∼1000 μatm, HC, High CO2) at 27°C (ambient) and 30°C (warming, HT, High Temperature). Our results indicate that warming, acidification, and their combined effects (HCHT) initially enhanced community biomass as determined by chl a concentration; however, this effect diminished over time, ultimately resulting in lower biomass density compared to the control in later stages. Primary productivity per volume of seawater in the HT and HCHT treatments was initially suppressed but increased in the later stages compared to the control group, whereas the HC treatment appeared to suppress it consistently. While higher effective photochemical efficiency and non-photochemical quenching coincided with higher photosynthetic carbon fixation per chlorophyll an under the HT and HCHT treatments, their decline under the HC after the acclimation was concurrent with decreased photosynthetic carbon fixation. Analysis of 18S rDNA revealed that diatoms and dinoflagellates dominated under the treatments of HC, HT, and HCHT, but compared to the control, the proportion of diatoms decreased by 23%, 14%, and6 %, while that of dinoflagellates increased by 19%, 9%, and 11%, respectively, under the corresponding treatments. Plankton richness increased under warming, while diversity declined, particularly with combined warming and acidification, highlighting community sensitivity to the stressors. With reference to heterotrophic microbes, the relative abundance of Basidiomycota increased by 16%–18% under HT or HCHT, along with insignificant impacts on prokaryotic communities based on 16S rDNA analysis. In conclusion, the combination of ocean acidification and warming treatment during the experimental period ultimately reduced the phytoplankton biomass density and altered the microbial community structure.
Continue reading ‘Combined effects of ocean acidification and warming on phytoplankton productivity and community structure in the coastal water of Southern East’Physiological and growth responses of Black Sea salmon (Salmo labrax) to long-term salinity and high carbon dioxide stress
Published 16 July 2025 Science ClosedTags: biological response, Black Sea, fish, fisheries, growth, laboratory, molecular biology, morphology, multiple factors, physiology, salinity
Black Sea salmon (Salmo labrax), an anadromous salmonid species of regional importance, is increasingly considered for aquaculture in the Black Sea. This study investigates the physiological and growth responses of Black Sea salmon to seawater transfer, with a particular focus on carbon dioxide (CO₂) stress. The experiment began on 5 July 2022 with 720 fish (76.68±15.34 g) reared under semi-controlled conditions using a freshwater recirculating aquaculture system (RAS). On 12 October 2022, a group of fish was transferred to Black Sea water (18 ppt), and a subgroup was exposed to elevated CO₂ (1000 µatm pCO₂) until the end of the trial on 7 March 2023. Exposure to carbon dioxide showed negligible or minimal effects on seawater adaptation and growth. In contrast, physiological markers such as gill Na⁺/K⁺-ATPase (NKA) activity and the expression of nkaα1a, nkaα1b, and nkcc1a genes, along with growth metrics—including specific growth rate (SGR), condition factor (K value), and liver gene expression of igf-I, igfbp1b, ghr1, and ctsl—indicated that the fish were not physiologically prepared for seawater transfer in autumn. These findings suggest that the commonly practiced autumn sea transfer in the region may lead to suppressed growth and suboptimal performance. The results emphasize the importance of aligning seawater transfer with the smoltification window to support fish health and optimize aquaculture outcomes in Black Sea salmon farming.
Continue reading ‘Physiological and growth responses of Black Sea salmon (Salmo labrax) to long-term salinity and high carbon dioxide stress’Impact of ocean acidification on skeletal structures in gilthead sea bream (Sparus aurata): in vitro and in vivo studies
Published 15 July 2025 Science ClosedTags: biological response, fish, growth, laboratory, Mediterranean, molecular biology, morphology, physiology
Highlights
- Ocean acidification affects bone mineralization.
- Ocean acidification modifies otolith size.
- Low extracellular pH increases the viability and mineralization of osteoblasts.
- Changes in cell culture pH modify the gene expression of osteoblasts.
Abstract
Ocean acidification is considered a significant risk to aquaculture, as it may adversely affect the growth and development of aquatic organisms. The effect of ocean acidification has been shown to impair the growth and survival of fish and to increase otoliths calcification in certain species; however, its effects on bone mineralization remain not well studied. The objective of the present study was to examine the effects of seawater acidification on the skeletal mineralization of gilthead sea bream juveniles, and to assess the direct impact of distinct pH levels on bone-derived cells development. After 68 days of exposure to low pH, fish exhibited a significantly reduced specific growth rate and elevated plasma pH levels, which influenced electrolyte concentrations such as potassium. Moreover, fish exposed to low pH showed increased otoliths size but no differences in shape. In bone, a higher vertebral length/height ratio was also observed, accompanied by significantly reduced opacity and increased expression of the osteoblast and osteoclast markers, alkaline phosphatase (alp) and matrix metalloproteinase 9 (mmp9), respectively, suggesting an elevated rate of bone turnover although reduced mineralization. In vitro, osteoblasts exposed to a low extracellular pH for 30 days exhibited increased viability and mineralization compared to cells maintained at a plasma pH or an alkaline pH. Additionally, the pH level significantly influenced the expression of several extracellular matrix components and osteoblast markers supporting those observations. Overall, these findings underscore the threat that ocean acidification poses to aquaculture, particularly through its impact on skeletal mineralization in gilthead sea bream, and highlight the importance of identifying approaches to farming resilient fish.
Continue reading ‘Impact of ocean acidification on skeletal structures in gilthead sea bream (Sparus aurata): in vitro and in vivo studies’Shifts in coral reef holobiont communities in the high-CO2 marine environment of Iōtorishima Island
Published 15 July 2025 Science ClosedTags: adaptation, biological response, BRcommunity, community composition, corals, field, molecular biology, North Pacific, otherprocess, phytoplankton, prokaryotes, vents
Ocean acidification (OA), driven by rising atmospheric CO2, presents a serious threat to marine biodiversity, especially within coral reef ecosystems. Natural analogue sites, such as the high-pCO2 seep at Iōtorishima Island in Japan, offer insights into future conditions. This study investigated the holobiont communities of Symbiodiniaceae and bacteria in the zoantharian Palythoa tuberculosa at Iōtorishima and compared them to specimens from control sites in Okinawa and Hawaiʻi. Using amplicon sequencing of the dinoflagellate internal transcribed spacer 2 (ITS2) region of ribosomal DNA and microbial 16S rRNA gene, we detected significant shifts in both Symbiodiniaceae and bacterial communities under high-pCO2 conditions at Iōtorishima. Specifically, P. tuberculosa at the seep site had reduced Symbiodiniaceae diversity, predominatly featuring Cladocopium C1 and C3 types. Additionally, its bacterial communities showed lower richness with distinct taxonomic profiles, including increased levels of Mollicutes and Vibrio spp. These results highlight the potentially adverse effects of OA on hexacoral holobionts and emphasize the need for detailed, high-resolution studies across various holobiont species and geographic locations. The shifts observed specifically in Symbiodiniaceae and bacterial communities at the Iōtorishima seep suggest that holobionts may exhibit plasticity in response to environmental stress, which has implications for resilience and adaptation of zoantharians and other reef organisms amid climate change. This research provides crucial baseline data for predicting future coral reef compositions in an OA-affected world.
Continue reading ‘Shifts in coral reef holobiont communities in the high-CO2 marine environment of Iōtorishima Island’Ocean acidification induces changes in circadian alternative splicing profiles in a coral reef fish
Published 14 July 2025 Science ClosedTags: biological response, fish, laboratory, molecular biology, South Pacific
Alternative splicing is a fundamental mechanism of gene expression regulation that increases mRNA diversity and can be partially regulated by the circadian clock. Time-dependent production of transcript isoforms from the same gene facilitates coordination of biological processes with the time of day and is a crucial mechanism enabling organisms to cope with environmental changes. In this study, we determined the impact of future ocean acidification conditions on circadian splicing patterns in the brain of fish, while accounting for diel CO2 fluctuations that naturally occur on coral reefs. The temporal splicing pattern observed across a 24-hour period in fish from the control group was largely absent in those exposed to either stable or fluctuating elevated CO2 conditions. Splicing patterns were influenced not only by an overall increase in CO2 concentration but also by its stability, with 6am and 6pm emerging as key timepoints when the majority of aberrant splicing events were identified. We found that fish in fluctuating CO2 conditions exhibited increased temporal plasticity in splicing events compared to fish in stable CO2 conditions. This was especially notable for genes associated with neural functioning. Our findings suggest that natural temporal splicing patterns in fish brains are disrupted by elevated CO2 exposure, with CO2 stability also influencing molecular responses. The increased plasticity in temporal splicing activity observed in fish in fluctuating CO2 environments may provide greater flexibility in biological responses to external pH changes, potentially enabling them to better cope with future ocean acidification conditions.
Continue reading ‘Ocean acidification induces changes in circadian alternative splicing profiles in a coral reef fish’Handling the heat: ocean acidification mitigates the effects of marine heatwaves on Posidonia oceanica seedlings
Published 8 July 2025 Science ClosedTags: biological response, laboratory, Mediterranean, mitigation, molecular biology, multiple factors, phanerogams, photosynthesis, physiology, reproduction, respiration, temperature
Ocean acidification (OA) and marine heatwaves (MHWs) are key drivers of marine ecosystem changes that can interact and influence marine organisms. Seagrasses, including the long-lived Posidonia oceanica endemic to the Mediterranean Sea, are widely distributed along coastal habitats, forming highly valuable underwater meadows. The germination and survival of the early life stages of P. oceanica are strongly affected by environmental changes. To assess the impact of warming and acidification on its future, we conducted a multifactorial experiment where P. oceanica seedlings were grown under OA conditions for six months and then exposed to a seawater warming event. Seedlings’ performance was investigated by analyzing photo-physiology, antioxidant capacity, energetic metabolism and transcriptomic profiles. The Weighted Gene Correlation Network Analysis (WGCNA) was used to integrate phenotypic plant traits with transcriptomic results to identify central genes involved in plant responses to OA and temperature exposure. Results demonstrated that prolonged OA exposure enhances P. oceanica seedling resilience to MHW. Specifically, seedlings regulated their antioxidant systems and transcriptomic machinery to better cope with thermal stress. Under current CO2 concentrations, elevated temperatures induced stress in P. oceanica seedlings, impacting photosynthesis and respiration. However, OA could mitigate the impact of warming in the future, enhancing P. oceanica‘s resilience to global stressors.
Continue reading ‘Handling the heat: ocean acidification mitigates the effects of marine heatwaves on Posidonia oceanica seedlings ‘Ocean acidity extremes retard shell formation of bivalve larvae: insights from transcriptomics and lipidomics
Published 2 July 2025 Science ClosedTags: biological response, laboratory, molecular biology, mollusks, morphology, North Pacific, physiology, reproduction
Highlights
- Effects of ocean acidity extremes (OAX) on early development of clams were assessed.
- OAX retarded shell formation of clam larvae.
- Reduced Ca2+ uptake and HCO3− production led to larval developmental retardation.
- OAX decreased cell membrane fluidity, limiting the uptake of calcification substrates.
- Larval shell formation under OAX was inhibited by depletion of energy reserves.
Abstract
In view of climate change and human activities, ocean acidity extreme (OAX) events have been increasingly reported worldwide over the last decades, which possibly retard the growth and development of marine organisms, particularly at their early life-history stages (e.g., embryos or larvae). Thus, understanding whether they can adjust to the sudden increase in seawater acidity has drawn growing attention. Using a commercially and ecologically important bivalve species (Ruditapes philippinarum) with a widespread distribution in the world, we assessed the impact of OAX on its embryonic and larval development as well as expressions of functional genes and lipids to indicate physiological and cellular performance. We found that embryonic development and larval shell formation were inhibited by OAX mainly due to the downregulation of key genes responsible for the uptake of calcium ions from ambient seawater (e.g., NCX, VGCC and SERCA) and the reduced production of bicarbonate ions through the catalytic action of carbonic anhydrase. In addition, a major remodelling in membrane lipids (e.g., PC, PE, PG, PI and PS) indicated that OAX impacted the fluidity and stability of cell membrane, hindering the uptake of calcification substrates. The depletion in energy reserves, such as triacylglycerol, can also account for the impairment in larval shell formation under OAX conditions. By integrating transcriptomics and lipidomics, our findings illustrate a novel molecular mechanism underlying the detrimental effect of OAX on larval development and hence population maintenance of marine organisms, which can have profound implications for sustaining ecosystem stability and aquaculture management.
Continue reading ‘Ocean acidity extremes retard shell formation of bivalve larvae: insights from transcriptomics and lipidomics’Phenotypic plasticity in Mediterranean gorgonians Eunicella singularis and Paramuricea clavata at high temperature and low pH
Published 2 July 2025 Science ClosedTags: adaptation, biological response, corals, laboratory, Mediterranean, molecular biology, multiple factors, otherprocess, performance, physiology, temperature
Highlights
- The oxygen consumption of the gorgonian corals increased at high temperatures.
- Energy reserves were not affected by high temperature, low pH or their interaction.
- The global DNA methylation in Eunicella singularis was not affected by high temperature, low pH, or their combination.
- Global DNA methylation in Paramuricea clavata decreased under high temperature and low pH.
- High temperature alone caused more DEGs in E. singularis than low pH or combined treatment.
Abstract
The Mediterranean gorgonian octocorals are threatened by acidification, warming and marine heat waves. Phenotypic plasticity is critical for slow-growing gorgonians, as adaptation through natural selection might not be fast enough to cope with rapid environmental changes. DNA methylation (DNAm) is a type of (trans)generational phenotypic plasticity mechanism that may help slow-growing corals better withstand the effects of environmental changes by adjusting gene expression. This study aimed to assess the physiological responses and epigenetic modifications associated with phenotypic plasticity in the Mediterranean gorgonians Eunicella singularis and Paramuricea clavata exposed to warming (+4 °C), acidification (−0.35 pHT units) and their combination over two weeks. In addition, RNA-Seq-based differential gene expression analysis was performed for E. singularis.
High temperature, low pH and their combination did not cause tissue death or necrosis in the corals. Polyp activity in E. singularis increased at high temperatures. Warming increased oxygen consumption in both species. Energy reserves (protein, lipid, carbohydrate contents) were not affected by temperature, pH or their interaction in either species. The global DNA methylation (gDNAm) rate was ten times higher in P. clavata than in E. singularis. There was no effect of temperature, pH or their interaction on gDNAm in E. singularis. gDNAm in P. clavata decreased at high temperatures and low pH. Differential gene expression analysis indicated that high temperature induced the most extensive transcriptional changes in E. singularis, while low pH alone had the least impact. The combined stress of high temperature and low pH also led to notable up- and downregulation of gene expression. Heat stress in E. singularis caused widespread downregulation of transcription factors (TFs), particularly those in the zf-C2H2, AP-2, and HMG families. Conversely, the IRF, RFX, P53, and NRF1 families were upregulated, highlighting the complex transcriptional response to thermal stress. Overall, these physiological, transcriptomic and epigenetic alterations have the potential to negatively impact the fitness of these emblematic species and their associated ecosystems.
Continue reading ‘Phenotypic plasticity in Mediterranean gorgonians Eunicella singularis and Paramuricea clavata at high temperature and low pH’Developmental and transgenerational effects of climate change on inorganic mercury toxicity in a marine copepod
Published 25 June 2025 Science ClosedTags: biological response, crustaceans, laboratory, molecular biology, multiple factors, North Pacific, oxygen, physiology, reproduction, zooplankton
Highlights
- Offspring/persistent OA plus OW aggravated IHg toxicity in T. japonicus.
- Persistent OA had stronger mitigating effect on IHg toxicity than offspring OA.
- OA plus OW intensified IHg toxicity in copepods mainly via lysosome dysfunction.
- Persistent OA enhanced energy metabolism and Hg efflux, decreasing IHg toxicity.
- Different scenarios of climate change can variably affect IHg toxicity in copepods.
Abstract
Dynamic shifts in multiple stressors are frequent in the marine environment. Here, we conducted a multigenerational experiment (F1-F4) to explore how different temporal scenarios of climate change, i.e., offspring/persistent ocean acidification (OA), warming (OW), and their combination (AW), could affect inorganic mercury (IHg) toxicity in the marine copepod Tigriopus japonicus. We found that persistent OA exhibited stronger mitigating effect on IHg toxicity in copepods than offspring OA, while offspring/persistent OW and AW aggravated its toxicity effects. We specifically performed transcriptomic analysis for the copepods of F4. Our transcriptomic result showed energy metabolism and detoxification were activated by persistent OA, enabling the copepods to resist IHg exposure. Instead, detoxification- and reproduction-related processes were inhibited in IHg-treated copepods under offspring/persistent OW and AW scenarios. Although apoptosis was suppressed to probably protect IHg-treated copepods under persistent AW, oxidative stress and lysosomal dysfunction ultimately caused reproductive impairment. Our study highlights that offspring/persistent (i.e., developmental/transgenerational) OA and OW could differentially modulate Hg toxicity in marine copepods, and more studies should focus on the temporal variation and complex interaction of multiple stressors, helping accurately project marine biota’s response in the future ocean.
Continue reading ‘Developmental and transgenerational effects of climate change on inorganic mercury toxicity in a marine copepod’Physiological and transcriptomic responses of Sargassum hemiphyllum to ocean acidification and nitrogen enrichment
Published 18 June 2025 Science ClosedTags: algae, biological response, laboratory, molecular biology, multiple factors, North Pacific, nutrients, physiology
Sargassum hemiphyllum 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 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 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 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 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 to ocean acidification and nitrogen enrichment’
