Coccolithophores, as calcifying phytoplankton, play a critical role in the global carbon cycle by producing calcium carbonate (CaCO 3 ) in the ocean through their calcitic coccoliths. Here we examine Gephyrocapsa huxleyi (formerly Emiliania huxleyi) and related species abundance and genetic diversity along the West Coast of North America from samples taken on the 2021 NOAA West Coast Ocean Acidification (WCOA21) cruise, along the margin from British Columbia, Canada, to San Diego, California, USA. Significant carbonate chemistry gradients were observed across 17 transects, mostly in the onshore-offshore and north-to-south direction. Abundance and morphometrics of Gephyrocapsa spp. was evaluated using real-time PCR of mitochondrial cytochrome c oxidase subunit 3 ( cox3 ) gene and by microscopy. Variation in PIC concentrations, G. huxleyi and related species abundance, and coccosphere thickness were found to be associated with the gradients in carbonate chemistry and nutrient concentrations (phosphate, nitrate, nitrite, ammonium) across stations sampled during the cruise. We identified 5 unique amplicon sequence variants (ASVs) of Gephyrocapsa spp. cox3 that systematically varied in relative abundance across the California Current System. Southern California locations had greater diversity in cox3 sequences than northerly locations. These analyses represent baselines for evaluation of the impacts of future environmental changes in coastal waters along this productive upwelling regime.
Continue reading ‘Coccolithophore genetic diversity, morphology, and contribution to particulate inorganic carbon production in Western North American coastal waters’Posts Tagged 'molecular biology'
Coccolithophore genetic diversity, morphology, and contribution to particulate inorganic carbon production in Western North American coastal waters
Published 27 April 2026 Science Leave a CommentTags: abundance, biogeochemistry, biological response, chemistry, field, molecular biology, morphology, North Pacific, phytoplankton
Ocean acidification induces neuronal hyperexcitation and anxiety-like behaviour in marine medaka via ASIC activation
Published 21 April 2026 Science Leave a CommentTags: biological response, fish, laboratory, molecular biology, performance, physiology
Ocean acidification presents a significant threat to marine life, yet its neurobiological mechanisms remain poorly understood. This study examined how acid-sensing ion channels (ASICs) mediate neuronal excitability and anxiety-like behaviour in marine medaka (Oryzias melastigma) under elevated CO2 concentrations (1000 and 1900 ppm). Transcriptomics revealed early upregulation of asic1a (4 days), while RT-qPCR demonstrated increased asic1a, asic1b, asic2 and asic4a (7 days), with only asic1a sustained at 30 days. Immunofluorescence confirmed heightened Asic2 in emotion-processing brain regions following acidification. Transmission electron microscopy unveiled distinct ultrastructural alterations: widened synaptic clefts, thinned postsynaptic densities, and decreased mitochondrial aspect ratios. Mitochondrial membrane potential assays revealed a reduction in membrane potential in response to acidification. Electrophysiological recordings showed increased neuronal firing count in the dorsolateral telencephalon under acidification, behavioural assessments revealed significant anxiety-like phenotypes, effects that were fully rescued by ASIC inhibition. These results indicated that temporal specificity in ASIC subtype expression in acidification response. The interplay of synaptic and mitochondrial dysfunction, neuronal hyperexcitability, and behavioural alterations suggested acidification impaired both synaptic transmission efficiency and mitochondrial function, destabilizing neural circuits. This study systematically elucidates the neurotoxic effects of ocean acidification on marine fish, providing critical scientific evidence for predicting the ecological impacts of climate change on marine organisms.
Continue reading ‘Ocean acidification induces neuronal hyperexcitation and anxiety-like behaviour in marine medaka via ASIC activation’Coexpression among eastern oyster host and microbiome genes suggests coordinated regulation of calcifying fluid chemistry
Published 13 April 2026 Science ClosedTags: biological response, BRcommunity, laboratory, molecular biology, mollusks, North Atlantic, physiology, prokaryotes
Significance
Oysters and many marine animals build shells by controlling the chemistry of extracellular fluids where minerals form, yet whether microbes in these fluids influence calcification remains unclear. We show that oysters maintain favorable conditions for mineral formation by regulating the carbonate chemistry of the shell-forming fluid, and that resident microbes respond to these changes by expressing nitrogen- and sulfur-cycling genes capable of altering pH, alkalinity, and carbonate availability. Many of these microbial transcripts were tightly correlated with oyster immune and signaling genes, suggesting that host and microbiome processes may be linked within the calcifying environment. These findings point to a host–microbiome interaction in the regulation of calcifying-fluid chemistry that directly links microbial activity to the carbonate chemistry underlying biomineralization.
Abstract
Marine animals that build shells, such as oysters, carefully regulate the chemistry of their internal calcifying fluids, but the molecular mechanisms behind this control, as well as whether microbes play a role in calcification, are poorly understood. To better understand oysters’ molecular mechanisms and the role of their calcifying-fluid microbes, we conducted experiments that simulated a tidal cycle, measured calcifying fluid pH and total dissolved inorganic carbon, and characterized host and microbial gene expression via transcriptomics. These experiments showed that calcifying fluid pH remained relatively stable throughout tidal pH fluctuations, with corresponding increases in oyster transcripts for ion transport and acid–base regulation. These data provide direct evidence that tidal fluctuations drive rapid changes in oyster calcifying fluid chemistry. Most surprisingly, increases in microbial transcripts related to nitrogen and sulfur cycling correlated to higher calcifying fluid DIC, and coexpression network analysis revealed patterns of gene expression that linked oyster immune and neural pathways to microbial redox processes, providing molecular evidence of potential host modulation of microbial metabolism. Together, these results reveal that oysters actively regulate their calcifying fluid pH over short timescales, and the endemic microbiome metabolic responses can yield metabolites that influence calcifying fluid pH, alkalinity, and ultimately calcification. These data offer a perspective on oyster physiological capacity and, most importantly, the potential role of microbes in oyster calcification. In light of ongoing changes in ocean pH and temperature, oysters provide a model for studying animal–microbial responses to environmental acidification and how their interactions may shape biomineralization.
Continue reading ‘Coexpression among eastern oyster host and microbiome genes suggests coordinated regulation of calcifying fluid chemistry’Intracellular acid-base regulation mediates a trade-off between shell and somatic growth in a clam under ocean acidification
Published 9 April 2026 Science ClosedTags: biological response, growth, individualmodeling, laboratory, mesocosms, modeling, molecular biology, mollusks, North Pacific, physiology
Highlights
- Clams actively regulate intracellular pH against ocean acidification via CAc
- RNAi confirms CAc’s essential role in H+ efflux, measured by in vivo SIET.
- A CAc-sAC-NKA network forms a conserved regulatory pathway for acid-base balance.
- DEB model shows this pH defense sustains shell linear growth despite metabolic costs.
SUMMARY
Ocean acidification (OA) is predicted to threaten marine bivalves, casting them as passive victims of changing carbonate chemistry. Contributing to a revised understanding, we identified a conserved mechanism for acid-base regulation that supports intracellular resilience. Using the Manila clam Ruditapes philippinarum as a model, this study demonstrated that intracellular pH (pHi) homeostasis under elevated pCO2 was maintained through cytosolic carbonic anhydrase (CAc)-mediated H+ efflux. A causal link was established by combining in vivo scanning ion-selective electrode technique (SIET) with RNA interference (RNAi), where RpCAc knockdown suppressed H+ efflux and compromised pHi. A coordinated regulatory network involving CAc, soluble adenylyl cyclase (sAC), and Na+/K+-ATPase (NKA) was synergistically upregulated, suggesting an evolved adaptive pathway. Dynamic Energy Budget (DEB) modeling, calibrated with experimental data, revealed that this cellular compensation carries a high energetic cost, leading to a significant reallocation of resources: shell growth was maintained, but somatic growth was severely suppressed. These results elucidate a conserved cytoprotective mechanism that enables short-term tolerance of OA at a substantial somatic cost, redefining resilience to include energetic trade-offs.
Continue reading ‘Intracellular acid-base regulation mediates a trade-off between shell and somatic growth in a clam under ocean acidification’Investigation of the adaptive mechanisms to ocean acidification in Patella species from CO2 vent systems of the Mediterranean Sea
Published 7 April 2026 Science ClosedTags: adaptation, biological response, field, Mediterranean, molecular biology, mollusks, morphology, otherprocess, physiology, respiration, vents
The continuous increase in anthropogenic carbon dioxide (CO2) emissions into the atmosphere is one of the main factors contributing to ocean acidification (OA). In fact, CO2 is partially absorbed by the oceans, where it alters carbonate chemistry and seawater pH, which is expected to decrease from the current level of 8.1 to 7.7 by 2100. OA exerts harmful impacts primarily on calcifying organisms, as it affects the availability of carbonates, which makes their calcareous structures thinner and more fragile. Moreover, several studies have described the detrimental effects of OA across many marine taxa, affecting important physiological and metabolic mechanisms. On the other hand, research conducted at CO2 vent systems, which are volcanic naturally acidified sites, showed that several organisms can survive under acidified conditions through specific tolerance and/or adaptive strategies. Among these organisms, the gastropod Patella spp. is one of the few calcifiers capable of inhabiting naturally acidified sites, such as the Castello Aragonese vent systems at Ischia Island and the San Giorgio vent systems at Sicily Island. Nonetheless, the complex mechanisms that allow survival and potential adaptation of these organisms to natural OA conditions need to be understood. Therefore, this PhD study aimed at investigating the potential molecular, physiological, metabolic, genetic, and epigenetic mechanisms that enable these organisms to tolerate and survive under OA conditions through a stepwise approach. Specifically, this PhD research attempted to answer the following questions: • Does OA entail a stressful condition in resident populations of Patella spp. living at reduced pH conditions, thereby affecting their overall well-being and health status? • Are there specific physiological, metabolic, and biochemical mechanisms that contribute in defining tolerance to OA? • Are limpets genetically adapted to OA? • Is DNA methylation contributing to promote tolerance to OA in limpets? • What is the role of environmental conditions in shaping the response to OA? The first chapter of this thesis considered three Patella species (P. caerulea, P. rustica, and P. ulyssiponensis) collected from the CO2 vent systems of the Castello Aragonese (Ischia Island). This vent system exhibits a natural acidification gradient ranging from ambient pH (N1: pH = 8.1), to intermediate pH (N2: pH = 7.7), and to extremely low pH (N3: pH < 7.4). Resident populations were collected along the gradient and at San Pietro, an additional ambient pH site (pH = 8.1), located at a distance of 4 km from the Castello vent. In addition, a 30-day in situ transplant experiment was conducted using P. caerulea, in order to evaluate the short-term responses induced by OA. Morphometric traits, such as shell length, height, width, and soft-tissue weight, were measured, and a set of biomarkers related to antioxidant system, energy metabolism, neurotoxicity, and biomineralization was applied. For resident populations, P. caerulea showed increased size and energy reserves at the extremely acidified site, likely related to a shift from erect calcified algae to biofilm, or to reduced competition and/or predatory pressure under acidified conditions. Biochemical endpoints measured in both P. caerulea and P. ulyssiponensis were not modified by OA. Conversely, P. rustica exhibited significant modulation of nearly all biochemical parameters, likely due to its different position on the rocky shore, which makes this species more exposed to tidal fluctuations and therefore to an additional source of disturbance, besides OA. Short-term exposure of P. caerulea to OA resulted in a decrease in protein content and an increase in glycogen content at the extremely acidified site, with the induction of superoxide dismutase and glutathione-S-transferase activities at intermediate pH, suggesting the activation of compensatory mechanisms to cope with reduced pH conditions. Overall, results revealed a distinct response to OA of the three species of Patella. Moreover, the increased size and energy-related endpoints observed in P. caerulea and P. rustica highlighted the need to further investigate energy metabolism aspects, in order to better understand the trade-offs between compensatory mechanisms and the energetic cost underlying tolerance to OA. Based on these evidences, the second chapter focused exclusively on P. caerulea, with the aim of deeply investigating metabolic and physiological stress-responses, comparing resident populations of the Castello Aragonese vent systems and transplanted organisms, similarly to the first chapter. Respiration and ammonia excretion rates were measured four times across the year. Additionally, untargeted metabolomics analyses were performed to investigate metabolic pathways potentially involved in response to OA. Only during summer, OA increased respiration rate in limpets from the most acidified site, while simultaneously reduced excretion rates, likely to allocate more energy resources to face the increasing temperature, besides OA. Furthermore, both resident and transplanted populations up-regulated carnitine metabolism, suggesting that OA induced an increase of energy production through β-oxidation and subsequent Krebs cycles. Moreover, several metabolites involved in osmoregulation, oxidative stress, and nucleic acid mechanisms were increased. Overall, results seem to confirm the presence of negative effects and of an energetic cost underpinning tolerance to OA. The third and final chapter investigated the potential influence of phenotypic plasticity, genetic adaptation, and DNA methylation in tolerance to OA in adult and juvenile populations of P. caerulea collected from two CO2 vent systems of the Mediterranean Sea. Adult and juvenile specimens were sampled along the acidification gradient of the Castello Aragonese vent systems of Ischia Island (San Pietro/N1: pH = 8.1; N2: pH = 7.7; N3: pH < 7.4) and from the San Giorgio vent systems of Sicily Island (Patti: pH = 8.1; San Giorgio: pH = 7.8). Following genomic DNA extractions from foot tissue and individual libraries preparation with the NEB Next® Enzymatic Methyl-seq Kit, samples were sequenced on the Illumina NovaSeq 6000 sequencer. Data processing and analyses were conducted on Euler platform mainly using biscuit tool, which enabled to simultaneously extract genomic and epigenomic information from DNA methylation sequencing. Population genomics and epigenomics analyses revealed divergent patterns between the Ischia and Sicily populations. Populations from the Ischia vent revealed marked signs of genomic differentiation, particularly in adults from the intermediate and extremely low pH sites, while reduced differences in DNA methylation levels were detected, especially in adults. These findings suggest a strong signature of purifying selection acting on standing genetic variation, through a within-generation response, likely driven by the more pronounced pH fluctuations occurring at these sites. Conversely, no genomic differentiation was observed between the Sicily populations, but greater differences in DNA methylation were detected between acidified and non-acidified sites at both adult and juvenile stages. These results revealed that this epigenetic mechanism, rather than genomic changes, may play a key role in the response to the milder pH variations of this vent and potentially enhance organisms’ tolerance to OA. In conclusion, this PhD project investigated tolerance to OA in limpets through a holistic approach that, for the first time, integrated morphological, physiological, metabolic, biochemical, genetic, and epigenetic analyses. Overall, findings revealed that Patella spp. has the ability to survive under acidified conditions even though with a physiological and metabolic cost, which could be partially compensated by more favorable environmental conditions. This study further highlights the importance of conducting research in naturally acidified environments, since it allows to formulate more realistic hypotheses about the ability of marine organisms to persist in future changing oceans.
Continue reading ‘Investigation of the adaptive mechanisms to ocean acidification in Patella species from CO2 vent systems of the Mediterranean Sea’Tolerance to future elevated CO2 conditions in sablefish (Anoplopoma fimbria), a deep-water benthic dwelling fish species
Published 26 March 2026 Science ClosedTags: biological response, fish, laboratory, molecular biology, North Pacific, performance, physiology
Numerous studies have found that elevated CO2 levels in marine waters induced significant physiological and behavioral effects in fish. In an earlier study of coho salmon (Oncorhynchus kisutch), we observed that elevated CO2 exposure impaired signaling in the olfactory bulb, through a mechanism likely involving interference of gamma-aminobutyric acid (GABA) signaling. However, the effects of elevated CO2 may be species-specific, and there have been few studies addressing the effects of elevated CO2 on benthic fish. In the current study, we investigated the effects of elevated CO2 exposures on the deep-water benthic species, sablefish (Anoplopoma fimbria). Sablefish were exposed to three different levels of CO2 (700, 1600 and 2700 µatm) for two weeks, followed by behavioral, neurophysiological and gene expression analysis of the olfactory system. Analysis of behaviors mediated by food odors, including swimming activity and food strikes did not differ between fish maintained under elevated or control CO2 conditions. Similarly, electro-olfactogram recordings of odorant signaling did not differ among treatment and controls. mRNA expression patterns of olfactory bulb genes that were altered in coho salmon exposed to elevated CO2 levels, were similarly examined in sablefish. Sablefish mRNAs encoding genes involved in GABA-mediated olfactory bulb signaling were generally unaffected by high CO2, but aldh9a1, an enzyme involved in the synthesis of GABA, was elevated by high CO2. The results of our study contrast other studies demonstrating adverse effects of elevated CO2 in pelagic fish, but support differences among fish species to susceptibility to elevated CO2, potentially associated with life history traits.
Continue reading ‘Tolerance to future elevated CO2 conditions in sablefish (Anoplopoma fimbria), a deep-water benthic dwelling fish species’Ocean acidification disrupts the biomineralization process in the oyster Crassostrea virginica via intracellular calcium signaling dysregulation
Published 20 March 2026 Science ClosedTags: biological response, laboratory, molecular biology, mollusks, morphology, North Atlantic, physiology, reproduction
Calcium is a key component in the shell and skeleton structure, serving as a second messenger for regulating biomineralization across many species. Ocean acidification (OA) is well-studied for causing shell dissolution in marine bivalve species by disordering calcium deposition. However, the regulatory pathway of calcification affected by OA remains unclear. This study assessed eastern oyster (Crassostrea virginica) to determine how calcium signaling responds to elevated pCO2 and influences shell formation. Under elevated pCO2, increased calcium influx was found in mantle epithelial cells, followed by the upregulation of calmodulin, a primary sensor of intracellular calcium. Expression levels of shell matrix proteins (SMPs), representing shell construction conditions, were significantly upregulated in the CO2-induced mantle cells. Larval C. virginica exhibited developmental stage-dependent alterations in calcium signaling and SMPs disarrangement stimulated by pCO2. Pharmaceutical blockage of the calcium binding on calmodulin induced abnormal expression of downstream genes and shell matrix changes consistent with those caused by elevated pCO2. Restored SMPs expressions in CO2-treated mantle cells were achieved by rescuing the level of calcineurin, a downstream effector of calmodulin. These findings suggest that shell deformities under OA are primarily caused by the disruption of the calcium-calmodulin signaling pathway in mantle epithelial cells.
Continue reading ‘Ocean acidification disrupts the biomineralization process in the oyster Crassostrea virginica via intracellular calcium signaling dysregulation’Influence of ocean warming and acidification on juveniles of the true giant clam, Tridacna gigas, and its microalgal symbionts
Published 19 March 2026 Science ClosedTags: biological response, BRcommunity, laboratory, molecular biology, mollusks, mortality, multiple factors, North Pacific, phytoplankton, reproduction, temperature
Uncontrolled carbon dioxide emissions from human activities contribute to ocean warming and acidification. These alterations in ocean chemistry threaten marine organisms, such as the true giant clam, Tridacna gigas, which is already imperiled due to overharvesting and habitat destruction. To gain an understanding of the physiological and molecular responses of T. gigas and its symbiotic dinoflagellates to ocean warming and acidification, we subjected juvenile individuals to different treatments simulating predicted seawater pH (7.6 and 8.0) and temperature (28°C, 30°C, 32°C and 34°C) levels for the next century. Juvenile giant clams were able to tolerate sustained exposure to temperatures of up to 32°C and pH as low as 7.6, while exposure to higher temperature (34°C), regardless of pH level, resulted in total mortality after a week. However, symbiosis was compromised even in the sublethal treatments, as indicated by the decrease in Symbiodiniaceae density and changes in symbiont gene expression. Symbionts significantly upregulated genes involved in splicing, translation, fatty acid metabolism, and DNA repair, which may constitute an adaptive response, while downregulating genes involved in photosynthesis and transmembrane transport, suggests impaired transfer of photosynthates to the host. These findings demonstrate the vulnerability of the juvenile T. gigas holobiont to heat stress, highlighting the critical importance of continued conservation and management alongside efforts to mitigate global changes in ocean conditions to safeguard this iconic marine bivalve.
Continue reading ‘Influence of ocean warming and acidification on juveniles of the true giant clam, Tridacna gigas, and its microalgal symbionts’Differential impacts of ocean acidification and alkalinization on shell microstructure and molecular responses in Mytilus edulis
Published 18 March 2026 Science ClosedTags: biological response, laboratory, molecular biology, mollusks, morphology, mortality, North Pacific
Anthropogenic CO2 emissions are intensifying ocean acidification (OA), disrupting carbonate chemistry and threatening marine calcifiers such as mussels. Ocean alkalinity enhancement (OAE) has been proposed as a marine carbon dioxide removal (mCDR) strategy that can also mitigate OA, but its ecological safety for aquaculture species remains poorly understood. Here, we examined the short-term (21 days) responses of the blue mussel Mytilus edulis to OA (pH 7.3) and NaOH-based OAE (pH 9.0) using integrated shell microstructure analysis and transcriptomics. The results showed that while survival rates were unaffected, OA caused marked shell degradation and activated stress-related molecular pathways, whereas OAE enhanced shell integrity and stimulated growth-associated processes. Across treatments, a core set of biomineralization-related genes (e.g., VWA7, CA14, ALPL) exhibited expression shifts, suggesting central roles in carbonate homeostasis. In contrast, differential regulations of genes such as CA10 and VWDE revealed pH-specific responses. Notably, OAE induced minimal disruption of biomineralization and alleviated OA-related damage, highlighting its potential to support mussel aquaculture under future ocean conditions. While model simulations and plankton-scale experiments suggest global benefits of OAE, this study provides direct organism-level experimental evidence linking shell ultrastructure and transcriptomic responses under OA and OAE conditions. These findings offer mechanistic insights into mussel resilience and provide a critical empirical basis for evaluating the ecological safety of OAE as both a carbon sequestration strategy and a tool for sustainable aquaculture.
Continue reading ‘Differential impacts of ocean acidification and alkalinization on shell microstructure and molecular responses in Mytilus edulis’Multi-level holobiont dysregulation increases the ecological risk of combined ocean acidification and benzo[a]pyrene pollution to the reef-building coral Porites lutea
Published 17 March 2026 Science ClosedTags: archaea, biological response, BRcommunity, community composition, corals, laboratory, molecular biology, multiple factors, North Pacific, otherprocess, photosynthesis, physiology, phytoplankton, prokaryotes, toxicants
Highlights
- Combined ocean acidification and BaP induce holobiont dysregulation, evidencing by a decoupled Symbiodiniaceae proliferation and a collapse of the archaeal Nanoarchaeota-Halobacterota symbiosis.
- The coral host shifts its defense strategy from antioxidant capacity to cellular homeostasis, while the bacterial community increases functional redundancy, revealing a costly acclimation mechanism.
- The multi-level dysregulation demonstrates an underestimated ecological risk, highlighting that current single-stressor risk assessments are inadequate for protecting corals under complex pollution scenarios.
Abstract
Reef-building corals are increasingly threatened by the combined effects of global climate change and localized organic pollutants. However, the holistic impacts of co-exposure to ocean acidification (OA) and benzo[a]pyrene (BaP) on coral holobionts remain poorly understood. Here, we investigated the multi-level responses of the reef-building coral Porites lutea to short-term (7-day) exposure to OA (pH 7.80), BaP (10 µg/L), and their combination, by integrating physiological measurements with microbiome profiling (ITS2 and 16S rRNA). We found that combined stress was associated with a dysregulated response in Symbiodiniaceae, characterized by a significant increase in cell density without a parallel rise in chlorophyll content, suggesting a possible compensatory but inefficient proliferation response. Despite this, the dominant symbiont Cladocopium C15 remained stable. The bacterial diversity increased (e.g., enrichment of Ruegeria and Acanthopleuribacter, decline of Endozoicomonas), which may suggest enhanced functional redundancy, while the archaeal community was significantly restructured, most notably a marked decline of the putative obligate Nanoarchaeota–Halobacterota symbiosis. At the host level, combined stress was associated with suppressed antioxidant enzyme activities (SOD/POD) but upregulated genes related to protein folding (Hsp90) and calcium homeostasis (NCX1, VAMP4). These findings suggest a complex holobiont reconfiguration under combined stress, involving a stabilized core symbiont, altered microbiomes, and a shifted host defense strategy. Our study suggests that the ecological risk of combined OA and organic pollution may not be extrapolated from single-stressor responses, indicating the need to incorporate multi-stressor frameworks into coral reef risk assessments.
Continue reading ‘Multi-level holobiont dysregulation increases the ecological risk of combined ocean acidification and benzo[a]pyrene pollution to the reef-building coral Porites lutea’Marine heatwaves, ocean warming and acidification reshape reef fish gut microbiomes
Published 16 March 2026 Science ClosedTags: biological response, BRcommunity, community composition, field, fish, molecular biology, multiple factors, North Pacific, otherprocess, physiology, prokaryotes, temperature, vents
Extreme climatic events and gradual climate change are increasingly anticipated to interact and reshape ecological communities. However, the combined effects of ocean warming, acidification and marine heatwaves on host‐associated microbial communities and their potential role in host adaptation remain poorly understood. Here, we assessed shifts in gut microbiome communities and their associations with physiological performance in one tropical ( Abudefduf vaigiensis ) and one subtropical ( Microcanthus strigatus ) reef fish species, across three temperate reefs representing natural analogues of climate change: a present‐day baseline (‘cool reef’), a chronically warmed reef (‘warm reef’) and a reef experiencing combined warming and extreme acidification (‘extreme reef’). We also examined gut microbiome changes in A. vaigiensis before and during a severe marine heatwave. A. vaigiensis had lower gut microbiome evenness and diversity at the warm (43% and 44% decrease, respectively) and extreme (38% and 31% decrease) reefs compared to the cool reef, and its gut microbiome community shifted at the extreme reef with a 122% increase in abundance of opportunistic bacteria Vibrio. A. vaigiensis also had lower gut microbiome richness at the warm (42% decrease) and extreme (52% decrease) reefs during the heatwave compared to pre‐heatwave individuals. In contrast, M. strigatus showed higher microbiome evenness (99% increase) and diversity (98% increase) at the warm reef compared to the cool reef; however, these gains were lost at the extreme reef, with microbiome diversity and evenness returning to cool reef levels. Microbiome changes in both species were generally not associated with their physiological performance (protein content, oxidative stress, antioxidant capacity or body condition). Our findings suggest that marine heatwaves, ocean warming and acidification can reshape reef fish gut microbiomes, driving simplification in Abudefduf vaigiensis but distinct restructuring in Microcanthus strigatus . We conclude that climate‐driven microbiome reshuffling may alter host–microbiome relationships and functions in fishes in a future ocean.
Continue reading ‘Marine heatwaves, ocean warming and acidification reshape reef fish gut microbiomes’Temperature and pH-dependent potassium currents of muscles of the stomatogastric nervous system of the crab, Cancer borealis
Published 13 March 2026 Science ClosedTags: biological response, crustaceans, laboratory, molecular biology, multiple factors, North Atlantic, physiology, temperature
HIGHLIGHTS
- Cancer borealis stomach muscles are sensitive to temperature and pH.
- Warming or alkalizing hyperpolarizes fibers and reduces synaptic response amplitude.
- qRT-PCR detects K2P gene transcripts CbKCNK1 and CbKCNK2 in muscles.
- CbKCNK1 and CbKCNK2 are candidates for the temperature and pH-dependent conductances.
SUMMARY
Marine crustaceans such as the crab Cancer borealis experience fluctuations in temperature and pH, yet their stomatogastric neuromuscular system must remain functional for feeding. We examined 16 of ∼40 stomach muscle pairs and found that warming consistently hyperpolarized muscle fibers (∼10 mV per 10°C) and reduced excitatory junctional potentials and currents. Muscle responses were also strongly influenced by extracellular pH, with an optimal range between pH 6.7 and 8.8; outside this window, abnormal activity emerged. Voltage-clamp analysis of gastric muscle gm5b revealed a temperature- and pH-sensitive conductance with a reversal potential near the potassium equilibrium potential and insensitivity to tetraethylammonium and barium, arguing against classical voltage-gated potassium channels. Quantitative RT-PCR detected expression of two putative two-pore domain potassium (K2P) channels in these muscles. Together, these results suggest that muscle excitability in C. borealis is shaped by temperature- and pH-sensitive potassium currents consistent with contributions from K2P channels.
Continue reading ‘Temperature and pH-dependent potassium currents of muscles of the stomatogastric nervous system of the crab, Cancer borealis’Multifactorial neural disruption in the brain of the Senegalese sole (Solea senegalensis) under ocean acidification
Published 11 March 2026 Science ClosedTags: biological response, fish, laboratory, molecular biology, physiology
Global ocean acidification, driven by rising atmospheric CO2, threatens marine ecosystems and biodiversity, with increasing evidence of disruptive effects on fish neurobiology and behaviour. However, the precise mechanisms underlying these impacts remain largely unresolved. Here, we reveal how chronic exposure to future-predicted CO2 levels disrupts brain function in the marine teleost Solea senegalensis. Using an integrative approach combining electrophysiology, immunohistochemistry and transcriptomics, we demonstrate that elevated CO2 induce a complex multifaceted disruption in brain physiology.
Contrary to the prevailing GABAA receptor reversal hypothesis, which predicts Cl− loss and heightened excitatory signalling under high CO2, we observed increased Cl− and HCO3− in cerebrospinal fluid and suppressed neural excitability. Immunohistochemistry 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 simplistic models of ocean acidification impact, unveiling a cascading interplay of enhanced GABAergic inhibition, immune shifts, glial dysfunction, and disrupted timekeeping mechanisms, likely contributing to the behavioural impairments under high CO2.
Unlike prior studies relying on behavioural assays or direct physiological proxies, our integrative approach, combining direct cerebrospinal fluid ionic measurements, electrophysiology, immunohistochemistry and transcriptomics, unveils a multifactorial physiological cascade. Our work advocated for integrative neurophysiological frameworks to predict marine fish resilience and vulnerability in a rapidly changing ocean.
Continue reading ‘Multifactorial neural disruption in the brain of the Senegalese sole (Solea senegalensis) under ocean acidification’Sex-specific physiological-biochemical and multi-omics responses of Sargassum thunbergii to ocean acidification
Published 10 March 2026 Science ClosedTags: algae, biological response, laboratory, molecular biology, North Pacific, photosynthesis, physiology
Highlights
- A multi-omics study on sexual dimorphism of macroalgae under OA.
- Male S. thunbergii adopted a growth-oriented strategy under OA.
- Female S. thunbergii showed a defense-oriented survival strategy under OA.
- Fundamental trade-off between growth and defense underlay sex-specific responses.
Abstract
Ocean acidification (OA), driven by increasing atmospheric CO2 concentrations, poses significant threats to the ecologically important intertidal macroalgae. Multiple previous studies have indicated species-specific responses to OA, the sex-specific physiological-biochemical responses and underlying molecular mechanisms in dioecious macroalgae remain poorly understood. In this study, we investigated the responses of male and female Sargassum thunbergii to acidification treatment (2000 ppm CO2) by integrating physiological-biochemical, transcriptomic, and metabolomic analyses. Both sexes maintained photosynthetic performance, with increased maximum relative electron transport rates (rETRmax). Males exhibited a growth-oriented strategy, characterized by higher accumulation of storage compounds like triglycerides and up-regulation of genes related to the photosynthesis and biosynthesis pathways. In contrast, females displayed a survival-oriented strategy, with reduced carbon storage, increased soluble protein and phenolic substance contents, and up-regulation of genes related to defense- and stress-response pathways. These findings provided physiological-biochemical and molecular evidence for a growth and defense trade-off between male and female S. thunbergii under acidification treatment. Our study provided the mechanistic insights into the sex-specific responses of marine macroalgae to global climate change and highlighted the importance of accounting for sexual dimorphism in predicting the ecological resilience of intertidal macroalgae populations under future ocean conditions.
Continue reading ‘Sex-specific physiological-biochemical and multi-omics responses of Sargassum thunbergii to ocean acidification’Ocean acidification reduces diatom and photosynthetic gene abundance on plastic in an coastal bay mesocosm experiment
Published 25 February 2026 Science ClosedTags: abundance, biological response, BRcommunity, community composition, laboratory, mesocosms, molecular biology, North Pacific, otherprocess, phytoplankton, prokaryotes
Discarded plastics are accumulating in the global ocean and posing threat to marine life. The plastisphere – the community colonizing plastic surfaces – profoundly influences plastic’s environmental behavior, affecting its degradation and entry into marine food webs. Ocean acidification (OA) resulted from anthropogenic CO2 emissions, is also threatening marine ecosystems, but the effect of OA on the structure and ecological function of the plastisphere community remains poorly understood. Here, using a mesocosm experiment, we investigated the effects of OA on the plastisphere colonizing floating PET plastic bottles. The study was conducted using subtropical eutrophic coastal water from Southern China under two CO2 conditions: increased CO2 to 1000 μatm (HC) and ambient CO2 410 μatm (LC). Metagenomic sequencing of the plastic samples, after exposure for 32 days, showed striking changes in relative abundance of eukaryotes and bacteria caused by HC. There was a 75.3 % decrease in eukaryote read abundances at high CO2, most strikingly a 95.6% decrease in the relative abundance of diatoms. In addition, the relative abundance of genes involved in photosystem II light reactions and pigment synthesis decreased under high CO2 conditions. This suggests that OA could reduce the photosynthetic potential within the plastisphere. Shifts in plastisphere community structure and potentially diminished photosynthesis under OA could influence the food chains within plastisphere, plastic degradation, transportation, and carbon cycle involving plastics. Overall, our results suggest that OA can alter the functional ecology of the plastisphere, with potential implications for marine biogeochemical processes and food web dynamics in subtropical eutrophic coastal water.
Continue reading ‘Ocean acidification reduces diatom and photosynthetic gene abundance on plastic in an coastal bay mesocosm experiment’Pacific cod gene expression analysis reveals how changing oceans impact larvae
Published 20 February 2026 Press releases ClosedTags: biological response, fish, molecular biology, multiple factors, North Pacific, temperature
A new study used gene expression analysis to explore how temperature and ocean acidification affect Pacific cod larvae. Scientists discovered that larvae are equipped with genes that allow them to survive cool and acidified conditions. However, warming may cause mortality by depleting energy and triggering inflammatory responses. These mechanisms are possible links between changes in ocean conditions and the recruitment of young fish in the Gulf of Alaska Pacific cod population.
Decrease in Pacific Cod Population
Pacific cod is a highly valued commercial fishery, and cod also play a key role in the ecosystem as both predator and prey. However, cod populations in Alaska have declined in recent years. Decreased population size is likely linked to recent marine heat waves, and early life stages seem to be the most impacted. Scientists predict that marine heatwaves may be more common in the future and that ocean acidification will intensify, particularly at high latitudes.
Experiments have shown that Pacific cod are sensitive to temperature during their early life stages. Temperature influences how their eggs develop, how their bodies use energy, and how they grow and survive as larvae. We don’t know as much about the impacts of ocean acidification.
In a 2024 study at the NOAA Fisheries Alaska Fisheries Science Center, scientists raised Pacific cod from embryos to larvae at multiple temperatures (3°C, 6°C, 10°C). To examine the potential interaction between temperature and ocean acidification, they also raised them in water that replicated current ocean conditions and in more acidified conditions. This mimicked conditions projected for the end of this century. The study found that larval mortality was very high in warm water but the effect of acidification was more complex.
The effects of temperature and acidified conditions depended on the fish’s development stage. Scientists need to better understand how changing ocean conditions can affect important species like Pacific cod, and whether these species can adapt to these changes.
A Deeper Dive with Gene Expression
This new molecular study examined larvae to understand why heat wave temperatures might cause larvae to die at high rates. “Finding larvae that are dying in the field is very unlikely, but we were able to sample experimental larvae that we knew were dying rapidly due to warming,” said Emily Slesinger, researcher at NOAA’s Alaska Fisheries Science Center. They also sampled larvae exposed to other conditions. The experiments simulated more acidified water and colder temperatures which Pacific cod larvae currently experience in some regions and years. Slesinger continues, “The unique thing about this study’s approach is to look beyond whether these larvae live or die under different conditions, but to understand why through gene expression analysis.”
Continue reading ‘Pacific cod gene expression analysis reveals how changing oceans impact larvae’Short-term mechanisms, long-term consequences: molecular effects of ocean acidification on juvenile snow crab
Published 20 February 2026 Science ClosedTags: adaptation, biological response, crustaceans, laboratory, molecular biology, morphology, mortality, North Pacific, otherprocess, physiology, reproduction
Understanding how marine species tolerate acidified conditions is critical for predicting biological responses to ocean change. A recent one-year experiment (Long 2026) found that juvenile snow crab (Chionoecetes opilio) maintain growth and molting under acidification (pH 7.8, 7.5), and survival begins to decline only after ∼250 days under severe acidification (pH 7.5). In this companion study, we characterized whole-transcriptome responses after 8 hours and 88 days of exposure to identify molecular mechanisms underlying short-term tolerance and chronic effects of ocean acidification. The immediate transcriptional response involved strong activation of genes associated with mitochondrial metabolism and biogenesis, protein homeostasis, cuticle maintenance, and immune modulation, processes shared between moderate and severe treatments but of greater magnitude under severe acidification. After 88 days, expression patterns diverged, revealing sustained upregulation of stress- and damage-mitigation pathways in the severe treatment (pH 7.5) compared to the moderate treatment (pH 7.8). These findings indicate that crabs in severe acidification are likely to experience chronic OA stress that precedes outward physiological effects, and provides a mechanistic basis for delayed mortality. We further highlight potential early indicators of chronic acidification stress in snow crab, among which a gene likely coding for carbonic anhydrase 7 (CA7, GWK47_031192) appears to be the most promising biomarker.
Continue reading ‘Short-term mechanisms, long-term consequences: molecular effects of ocean acidification on juvenile snow crab’Molecular indicators of warming and other climate stressors in larval Pacific cod
Published 19 February 2026 Science ClosedTags: biological response, fish, molecular biology, morphology, multiple factors, North Pacific, reproduction, temperature
Recent marine heatwaves in the Gulf of Alaska negatively impacted Pacific cod (Gadus macrocephalus) through a series of failed year classes and poor recruitment to the fishery. Experimental work by Slesinger et al. (2024) corroborated the hypothesis that warming directly impacts recruitment by increasing larval mortality rates. In this companion study, we applied transcriptomics with larvae from Slesinger et al. (2024) to better understand how warming affected their physiology and identify potential mechanisms contributing to mortality. RNASeq data reveal that warm-exposed larvae have unique gene expression profiles that may reflect high levels of inflammation, lipid dysregulation or depletion, and altered development of visual systems and neurological pathways. Warming may therefore cause a metabolic mismatch whereby energy-demanding activities (development, inflammation, growth) exceed energy production capacity despite access to prey. We also report the less pronounced transcriptional differences in larvae exposed to cold, acidification, and a combination of stressors reflecting future climate scenarios. This information will guide future genetic and experimental work that will ultimately inform recruitment forecasts in years with conditions similar to those tested here.
Continue reading ‘Molecular indicators of warming and other climate stressors in larval Pacific cod’Population-level transcriptomic datasets from two benthic invertebrates exposed to long-term experimental warming and acidification
Published 18 February 2026 Science ClosedTags: biological response, laboratory, Mediterranean, molecular biology, mollusks, multiple factors, porifera, temperature
Ocean warming and acidification are major drivers of change in marine ecosystems, with particularly strong impacts on low-mobility benthic organisms. Despite their ecological importance, genomic and transcriptomic resources for sponges (Phylum: Porifera) and marine gastropods (Phylum Mollusca) that capture responses to long-term, combined climate stressors and population-level variability remain limited. Herein, we present population-level RNA-seq datasets from the sponge Chondrilla nucula and the gastropod Hexaplex trunculus, collected from northern and southern Aegean Sea (Eastern Mediterranean) populations and exposed for three months to elevated temperature and reduced pH in a common garden experiment simulating near-future climate change conditions. The datasets comprise high-quality paired-end Illumina reads, a complete de novo transcriptome assembly for C. nucula, and genome-guided alignments for H. trunculus. These datasets provide a valuable resource for investigating transcriptional plasticity and climate change resilience in benthic marine invertebrates.
Continue reading ‘Population-level transcriptomic datasets from two benthic invertebrates exposed to long-term experimental warming and acidification’Microbial community dynamics over large spatial and environmental gradients in a subtropical ocean basin
Published 9 February 2026 Science ClosedTags: abundance, biogeochemistry, biological response, chemistry, community composition, field, molecular biology, North Atlantic, otherprocess, prokaryotes, protists
Microbes are fundamental to ocean ecosystem function, yet they remain understudied across broad spatial and environmental scales in dynamic regions like the Gulf of America/Gulf of Mexico (GOM). We employed DNA metabarcoding to characterize prokaryotes (16S V4–V5) and protists (18S V9) across 51 stations, spanning 16 inshore–offshore transects and three depths. Cluster analysis revealed three clusters corresponding to depth zones that integrated vertical and horizontal sampling: photic zone (inshore near surface–bottom and offshore surface), deep chlorophyll maximum (offshore), and aphotic zone (offshore near bottom). We applied group-specific generalized additive models (GAMs) to log-transformed abundance data of major taxa in the photic zone, identifying key environmental factors that explained 42%–82% of the variation in abundance. SAR11 and SAR86 were positively associated with temperature and dissolved inorganic carbon, while cyanobacterial genera (Prochlorococcus and Synechococcus) were differently impacted by nutrients, salinity, and pH in ways that often followed their expected ecological niches. Representatives of protist parasites (Syndiniales) and grazers (Sagenista) showed group-specific nonlinear associations with salinity, oxygen, nutrients, and temperature. Using GAMs, we expanded the spatial resolution of DNA sampling and predicted surface log abundances at 84 cruise sites lacking amplicon data. Indicator analysis was performed with sequence-level data, revealing several protists that were indicative of more acidic waters and the absence of any significant prokaryote indicators. Our results provide the first basin-scale survey of microbes in the GOM and highlight the need for coordinated omics and environmental sampling to improve predictions of microbial responses to changing conditions.
Continue reading ‘Microbial community dynamics over large spatial and environmental gradients in a subtropical ocean basin’
