Posts Tagged 'molecular biology'

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Phenotypic plasticity in Mediterranean gorgonians Eunicella singularis and Paramuricea clavata at high temperature and low pH

Published 2 July 2025 Science Closed
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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.

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Developmental and transgenerational effects of climate change on inorganic mercury toxicity in a marine copepod

Published 25 June 2025 Science Closed
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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.

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Physiological and transcriptomic responses of Sargassum hemiphyllum to ocean acidification and nitrogen enrichment

Published 18 June 2025 Science Closed
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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.

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Positive interactions in a warmer and more acidic ocean: crustose coralline algae holobionts enhance gorgonian larval settlement under climate change

Published 21 May 2025 Science Closed
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Background: The increasing frequency of marine heatwaves is leading to mass mortality of gorgonians in the Mediterranean Sea, threatening some populations with local extinction. A better understanding of the dynamics of gorgonians’ early life stages under climate change is urgent to ensure their conservation. Crustose coralline algae (CCAs) and their associated bacteria are known to induce the larval settlement of several coral species through the production of chemical cues. The larvae of the white gorgonian Eunicella singularis have been observed to preferentially settle and metamorphose on CCAs. Here, we investigated this positive interaction, and explored how it might be altered by climate change. Specifically, we tested the capacity of two Mediterranean CCA holobionts, Macroblastum dendrospermum and Lithophyllum stictiforme, to foster E. singularis larval settlement after exposure to SSP5-8.5 projected conditions for 2100 (warming and acidification), combined or not with a simulated marine heatwave event.

Results: Our results showed a threefold increase of larval settlement in presence of the CCAs previously exposed to acidification and warming treatments. After these treatments, both CCAs hosted a consistently high abundance of bacteria belonging to the Pirellulaceae family, and exhibited a higher abundance of monosaccharides in their exudates. We hypothesize that the enhanced larval settlement was driven by the bacterial breakdown and utilization of CCA polysaccharides, in combination with their release through the CCA cell walls. This release may have been enhanced by a decalcification process induced by climate change conditions. Furthermore, we showed that CCAs act as sources of bacterial taxa that can establish and persist in adult E. singularis holobiont, independently of climate change effects.

Conclusions: Our results highlight that CCA-larvae interaction is critical for E. singularis recruitment success, especially under future climatic conditions, and influences the development of its microbiome. This research underscores the importance of studying positive interspecific interactions across biological levels (from microorganisms to macroorganisms) under climate change scenarios, and provides valuable insights that inform the conservation and restoration of the Mediterranean white gorgonian.

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Exploring the land-ocean biogeochemical and microbial connectivity in the Ría de Vigo (NW Iberian Peninsula) through submarine groundwater discharge

Published 20 May 2025 Science Closed
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Highlights

  • SGD affects the carbonate system, methane and nitrous oxide content of the embayment
  • Solute composition of SGD largely impacted by subterranean estuary reactivity
  • Contrasting poor microbial connectivity across the different aquatic environments
  • Subterranean estuaries may act as microbial boundaries in the aquatic continuum

Abstract

Increasing evidence demonstrates the widespread occurrence of submarine groundwater discharge (SGD) in coastal zones, where it may influence biogeochemistry and microbial ecology. Here, we analyze the biogeochemical composition and microbial communities across diverse aquatic environments in a highly productive coastal system (Ría de Vigo, NW Iberian Peninsula), influenced by significant fresh SGD, to assess the extent of microbial and biogeochemical connectivity—i.e., mass transfer—among them. Samples were collected from surface and deep porewaters from two subterranean estuaries (STEs), surface seawater, riverine water, and continental groundwater. These samples were analyzed for a comprehensive set of microbial and biogeochemical variables, including radioisotopes used as SGD tracers. A significant correlation between SGD tracers and carbonate system parameters, N2O, and CH4 concentrations in surface seawater indicates SGD influences biogeochemistry of the embayment. However, some of these solutes do not originate from continental groundwater but are produced in the local STEs, which act as biogeochemical reactors modifying fresh SGD. The findings also reveal highly diverse microbial communities, with higher diversity in STEs due to the variety of niches present. Indicator taxa included the phyla Euryarchaeota, Chloroflexi, Omnitrophicaeota, and the family Nitrosopumilaceae in STEs; the phylum Cyanobacteria and the family Burkholderiaceae in freshwater endmembers; and the Flavobacteriaceae and Cryomorphaceae families in seawater. Most operational taxonomic units (∼87%) were unique to a single environment (river, continental groundwater, coastal water, or STE), showing STEs limit subterranean microbial transfer between groundwater and marine ecosystems. Our results highlight STEs as reservoirs of diversity and zones of intense biogeochemical reactivity.

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Hydrothermal vents as observatories for future ocean acidification (OA) scenarios: an in-situ study to unravel the involvement of ATP binding cassette transporters in the adaptation of marine polychaetes Platynereis spp. to OA

Published 16 May 2025 Science Closed
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The marine annelid Platynereis dumerilii, is a key model in genetics, evolution, neurobiology, ecology, and ecotoxicology. Along with its sibling species, P. cfr massiliensis, it thrives in both normal and naturally acidified environments. This makes these species ideal candidates for studying mechanisms of tolerance to acidified conditions, resembling future ocean acidification (OA) scenarios. The ATP-binding cassette (ABC) transport proteins help mitigating the adverse impacts of drugs, xenobiotics and physical stressors. There is growing evidence for their involvement to mediate tolerance towards acid-stress in bacteria and tumor cell lines. Such a function may be relevant for the ability of marine species to cope with OA and may be important to consider when predicting future OA scenarios for marine fauna. Here we addressed the question if ABC transporters of Platynereis spp. are involved in compensating adverse effects of low pH by studying ABC transporter transcript levels in marine animals exposed to various pH levels. We firstly examined P. dumerilii whole genome data (version EMBL_pdum_1.0, Genbank assembly: GCA_026936325.1) for the presence of ABC transporter genes, by homology searches, and, using the single-cell atlas database with P. dumerilii gene expression data, we then determined the presence of a potentially relevant subset of ABC transporters from the ABCB, C and G subfamilies in different organs/tissues. Finally, to assess how seawater pH affects ABC transporter expression, we conducted an in-situ reciprocal transplant experiment involving individuals of P. dumerilii/P. cfr massiliensis. Adult specimens were collected inside and outside the CO2 vents off Castello Aragonese (Ischia Island, Italy). Individuals collected from normal pH areas (8.18 ± 0.005) were transplanted to acidified conditions (7.33 ± 0.312), and vice versa, while others were placed in their original areas. We found 81 orthologs from ABC transporter subfamilies A-G, expressed in different organs/tissues including midgut, neurons, body epidermis and ectodermal cells, and somatic and visceral muscle. Following the 30 days transplant experiment, qPCR analyses were performed to examine the expression levels of seven selected genes from the ABCB, ABCC, and ABCG subfamilies (abcb_1, abcb_2, abcb_3, abcc_1, abcc_2, abcc_3, and abcg). Three of these genes were differentially expressed in specimens transplanted from normal pH to low pH areas (abcb_1 and abcg up-regulated while abcb_3 down-regulated). Based on the homology with human ABCB1 and ABCG2, which are crucial in tumor cell adaptation to acidified environments, it seems reasonable to hypothesize that abcb_1, abcb_3 and abcg play a similar role in Platynereis spp. helping in maintaining cellular homeostasis and surviving acid stress.

Continue reading ‘Hydrothermal vents as observatories for future ocean acidification (OA) scenarios: an in-situ study to unravel the involvement of ATP binding cassette transporters in the adaptation of marine polychaetes Platynereis spp. to OA’

Comparative transcriptomic analysis reveals a differential acid response mechanism between estuarine oyster (Crassostrea ariakensis) and Pacific oyster (Crassostrea gigas)

Published 2 May 2025 Science Closed
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Highlights

  • Mechanisms underlying resilience of estuarine oysters to low pH were analyzed.
  • Estuarine oysters have evolved enhanced acid-tolerance responding to low pH levels.
  • Frontloaded genes contributing to the enhanced acid-tolerance of estuarine oysters.
  • Ion transporters and translation are crucial in mitigates low pH effects in estuarine oysters.
  • Acid adaptation of estuarine oysters offers new insights into the adaptive potential of mollusks.

Abstract

Ocean and coastal acidification (OCA) poses a significant and rapidly emerging threat to mollusks. The physiological resilience of mollusks to OCA varies considerably; however, the underlying molecular mechanisms remain poorly understood. Seawater in estuaries, being more susceptible to acidification than that in open coastal zones, may enhance the tolerance of resident mollusks to low pH levels. Here, we conducted a comparative analysis between estuarine oysters (Crassostrea ariakensis) and Pacific oysters (Crassostrea gigas) using physiological phenotype and transcriptomic analyses to reveal differential acid-tolerance mechanisms in response to constant pH of 7.8. Our findings indicated that survival and respiration rates of C. ariakensis, which inhabits estuaries with fluctuating pH levels, were higher than those of C. gigas, which inhabits open coastal zones with relative stable pH conditions. Acid-responsive genes identified in C. gigas, including molecular chaperones and immune-related genes, exhibited higher constitutive expression in C. ariakensis under control conditions. Co-expression analyses revealed that C. ariakensis mitigated the effects of low pH by expressing genes involved in ion transporter activity and translation control. C. gigas activated genes associated with glycolipid metabolism while inhibiting cell division during acid stress. These findings suggested that C. ariakensis has evolved into a more energy-efficient regulatory network than C. gigas, incorporating both front-loading and responsive mechanisms to maintain acid-base homeostasis. This study is the first to investigate acid-tolerance differences between mollusks inhabiting estuarine and open coastal environments and provides critical insights into the resilience of mollusks in increasingly acidified oceans.

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Low-pH conditions drive transient changes in shell calcification and the microbiome in a pH-resistant strain of the the Pacific oyster Magallana gigas

Published 29 April 2025 Science Closed
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The study explores the effects of elevated pCO2 on shell calcification, microbiome composition, and gene expression in a strain of Pacific oyster (Magallana gigas) selectively bred for low-pH resistance. Juvenile oysters reared under low-pH conditions exhibited increased shell mass compared to the control population by 51 days post-fertilization, despite high variance in shell size at earlier stages. Microbiome analyses revealed significant shifts in community composition under low-pH conditions, particularly in bacterial taxa involved in CO2 production and biogeochemical cycling, which could influence carbonate chemistry within oyster tissues. Gene expression profiling demonstrates differential regulation of genes related to biomineralization, immunity, and microbial interactions under low-pH conditions. For example, multiple carbonic anhydrases exhibited treatment-specific expression patterns, suggesting a role in adapting to low-pH environments. Observed changes in immune-related genes imply a relaxation of immune responses, potentially reflecting resource reallocation toward calcification processes. These results collectively support the “dysbiosis hypothesis,” where oysters adapt to environmental stress by modulating their microbiomes and gene expression. Future studies should investigate whether these responses are consistent across oyster strains and environmental conditions, providing insights into the resilience of aquaculture species to ocean acidification.

Continue reading ‘Low-pH conditions drive transient changes in shell calcification and the microbiome in a pH-resistant strain of the the Pacific oyster Magallana gigas’

Initiation of bivalve shell calcification under ocean acidification: integrating insights from shell to cell

Published 9 April 2025 Science Closed
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The formation of initial bivalve shell is sensitive to ocean acidification, encoding the basis of shell formation and environmental information. Here, we demonstrated how the initial shell building processes were affected under various acidified conditions. With decreasing pH, larvae showed smaller shells and higher incidences of deformity. Shell elemental and isotopic profiles suggested that larvae almost exclusively used seawater dissolved inorganic carbon to calcify and exhibited diminished ability to maintain the calcifying fluid homeostasis. Compared to those reared at pHNBS 8.1, larvae exposed at pHNBS 7.7 downregulated the expression of genes related to transport of calcification substrates and regulation of carbonate chemistry, all of which were subsequently upregulated at pHNBS 7.4. This integrated finding advances the application of sclerochronology by providing insights into the initial shell formation, a crucial phase that is overlooked in sclerochronological studies, particularly in how environmental stressors affect the interpretation of geochemical proxies in adult shells.

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Molecular evidence for the intermediate disturbance hypothesis in an acidified marine system

Published 25 March 2025 Science Closed
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The Intermediate Disturbance Hypothesis (IDH), postulated by Connell (1978), suggests that ecosystems exhibit higher species diversity when disturbances occur at intermediate scales. In this study, the applicability of the IDH at the intraspecific scales (organismal) was investigated using molecular data. As an experimental perturbation framework, a naturally acidified system located in La Palma Island, Canary Island (Spain) with a sharp fluctuating pH gradient was sampled. Molecular data were obtained from sequences of a fragment of the mitochondrial Cytochrome C Oxidase subunit I gene in two sea urchin species (Arbacia lixula and Paracentrotus lividus) to explore genetic diversity at the organism level. These data were compared with previous metabarcoding results of taxonomic benthic diversity at the community level. Both sea urchin species showed the highest levels of haplotype and nucleotide diversity at the intermediate pH fluctuation zone, mirroring metabarcoding data that revealed the highest levels of taxonomic diversity at the same zone. The results support the validity of the IDH in marine ecosystems affected by strong pH fluctuations and across different levels of biological organization (from organisms to communities).

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Uncertain fate of pelagic calcifying protists: a cellular perspective on a changing ocean

Published 26 February 2025 Science Closed
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Pelagic calcifying protists such as coccolithophores and foraminifera represent an important microbial component of the marine carbon cycle. Although their calcitic shells are preserved in oceanic sediments over millennia, their resilience in the future decades is uncertain. We review current literature describing the response of calcifying protists to ocean acidification and temperature warming. We examine these key ecological and biogeochemical processes through the cellular perspective, exploring the physiological, metabolic, and molecular responses of calcifying protists. Ocean acidification is a chemical process that takes place in the seawater outside the cell, whereas protists calcify inside a modified cellular microenvironment. The function of these calcification compartments depends on cellular response to ocean acidification, such as maintaining pH homeostasis. The response of calcifying protists to ocean acidification and temperature warming is species-specific, with no unifying trends but rather a range of sensitivity levels. Coccolithophores and foraminifera display physiological sensitivity that may hamper their ecological success in comparison to non-calcifying species. Yet, certain species may be more adaptable, especially when comparing to highly vulnerable calcifying molluscs as pteropods. As the molecular machinery mediating cellular calcification is not fully resolved, as well as the functional role of the calcitic shell, our ability to predict the fate of calcifying microorganisms in a warmer, more acidic ocean is limited. We propose the urgent need to expand the study of these model systems by advancing cell biology approaches, to better understand the impact of climate change on microbial food webs in the ocean.

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The nasal microbiota of two marine fish species: diversity, community structure, variability and first insights into the impacts of climate change-related stressors

Published 25 February 2025 Science Closed
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Vertebrate nasal microbiota (NM) plays a key role regulating host olfaction, immunity, neuronal differentiation, and structuring the epithelium. However, little is known in fish. This study provides the first comprehensive analysis of the NM in two marine fish species, the European seabass and the Atlantic cod. Given its direct environmental exposure, fish NM is likely influenced by seawater fluctuations. We analysed the community structure, specificity regarding seawater, and interindividual variability of 32 to 38 fish reared under ambient conditions. Additionally, we conducted an experiment to investigate the influence of acidification and a simplified heatwave on cod NM (3 fish per replicate). High-throughput 16S rRNA sequencing revealed species-specific NM communities at the genus-level with Stenotrophomonas and Ralstonia dominating seabass and cod NM, respectively. This suggests potential habitat- or physiology-related adaptations. The most abundant bacterial genera in seabass NM were also present in seawater, suggesting environmental acquisition. Alpha diversity was highest in Brest seabass NM and variability greatest in Tromsø cod NM. Simulated climate change-related scenarios did not significantly alter cod NM structure. We propose a minimum of 13 cod rosettes per replicate for future studies. This research establishes a foundation for understanding marine fish NM and its response to environmental changes.

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Transcriptomic reaction norms highlight metabolic depression as a divergence in phenotypic plasticity between oyster species under ocean acidification

Published 21 February 2025 Science Closed
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Ocean acidification occurs at a rate unprecedented for millions of years, forcing sessile organisms, such as oysters, to respond in the short term by relying on their phenotypic plasticity. Phenotypic plasticity has limits, tipping points, beyond which species will have to adapt or disappear. These limits could be related to the adaptation of species to different habitat variabilities. Here we expose juvenile pearl oysters, Pinctada margaritifera, to a broad range of pH and determine the response at the gross physiological, lipidome and transcriptome levels. Thus, we identify its high tolerance with low tipping points at pH 7.3-6.8 below which most physiological parameters are impacted. We then compare the transcriptomic reaction norms of the tropical subtidal P. margaritifera, with those of an intertidal temperate oyster, Crassostrea gigas, reusing data from a previous study. Despite showing similar tipping points with C. gigas, P. margaritifera exhibits strong mortalities and depletion of energy reserves below the tipping points, which is not the case for C. gigas. This divergence relies mainly on the induction of metabolic depression, an adaptation to intertidal habitats in C. gigas, but not in P. margaritifera. Our method makes it possible to detect divergences in phenotypic plasticity, probably linked to the species’ specific life-history strategies related to different habitats, which will determine the survival of species to ongoing global changes. Such an approach is particularly relevant for studying the physiology of species in a world where physiological tipping points will be increasingly exceeded.

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Transcriptome and lipidome integration unveils key mechanisms constraining bivalve larval sensitivity in an acidifying sea

Published 21 February 2025 Science Closed
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Highlights

  • OA inhibits key ion transport required for larval calcification.
  • OA induces major remodeling of membrane lipids in larvae.
  • OA exerts distinct inhibitory mechanisms on larval shell formation.

Abstract

The intensity, frequencye and duration of seawater acidification in coastal seas have already surpassed projections for open oceans. Bivalve larvae are extremely sensitive to intensifying coastal seawater acidificaiton during their initial shell building, a critical period constraining recruitment success and population maintenance, but underlying mechanisms of larval shell formation sensitivity to acidification remain largely debated. Here, we performed an integrated analysis of the transcriptome and lipidome of trochophore of Ruditapes philippinarum to compare the core molecular responses involved in initial shell formation under ambient (pH 8.1), moderately (pH 7.7), and severely (pH 7.4) acidified conditions. Ocean acidification (OA) affected the ion transport efficiency by inhibiting gene expression of key ion transporters, thereby inhibiting initial shell formation, but the gene downregulation in the moderate exposure group was more significant. OA also induced major membrane lipid remodeling in larvae, which also significantly affected the ion transport efficiency. The TAG content of larvae which sustained the energy supply for active transport of calcification substrates and synthesis of organic matrix in the severe exposure group was significantly reduced. Overall, OA inhibited the formation of the initial larval shell, but different levels of OA had different inhibitory mechanisms on the initial larval shell formation, and the present study also further identified the role of lipids in initial shell formation, which can provide a theoretical basis for for a more accurate and comprehensive assessment of the impact of OA on bivalve calcification in an acidifying ocean.

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Transcriptome‐to‐phenome response of larval Eastern oysters under multiple drivers of aragonite undersaturation

Published 19 February 2025 Science Closed
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Understanding how interactive environmental challenges affect marine species is critical to long‐term ecological and economic stability under global change. Marine calcifiers are thought to be vulnerable to ocean acidification (OA; elevated pCO2); active dissolution of aragonite (Ωar) is associated with disrupted development, survivorship, and gene expression in bivalve larvae, resulting in an early life‐stage bottleneck. Dynamic carbonate chemistry in coastal systems emphasizes the importance of multiple stressors, e.g., warming and low salinity events may change organismal responses relative to OA alone. We exposed Eastern oyster larvae ( Crassostrea virginica ) to a full‐factorial experimental design using two temperatures (23°C and 27°C), salinities (17 and 27), and pCO2 levels (~700 μatm and 1850 μatm pCO2), resulting in Ωar conditions 0.3–1.7. Ωar reduced by low salinity, elevated pCO2, and low temperature, each slowed early development and reduced survival. Low salinity × elevated pCO2 was linked to severe Ωar undersaturation (< 0.5) that suppressed expression of bicarbonate transport, biomineralization and augmented expression for ciliary locomotion, proteostasis, and histone modifiers. In isolation and under moderate Ωar intensity (0.5 < Ωar < 1), larvae increased transcription for osmoregulatory activity and endocytosis under low salinity, and suppressed transcription for iron metabolism under elevated pCO2. Although shell growth and survival were affected by Ωar undersaturation, gene expression patterns of D‐stage oyster larvae and oyster juveniles suggests tolerance to dynamic estuarine environments. Genes and expression patterns that confer survival of postmetamorphosed oysters can improve our understanding of environmental‐organismal interactions and improve breeding programs enabling sustainable production.

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Olfactory specialization in the Senegalese sole (Solea senegalensis): CO2 acidified water triggers nostril-specific immune processes

Published 10 February 2025 Science Closed
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Highlights

  • Exposure to high PCO2/low pH water decreases olfactory sensitivity in sole more markedly in the upper olfactory epithelium (OE).
  • Resilience of the lower OE may be linked to exposure to a different environment.
  • Regulation of genes related to neuromodulation and neuroplasticity suggests activation of compensatory mechanisms.
  • Regulation of immune processes related genes together with histological modifications will likely compromise olfactory sensitivity with behavioural consequences.
  • Ocean acidification has effects on the peripheral nervous system at various levels.

Abstract

Increased carbon dioxide (CO2) in the ocean is changing seawater chemistry. Behavioural alterations in CO2 exposed fish have been linked to changes in the central nervous system (CNS). However, we hypothesise that receptor cells in direct contact with the environment are more susceptible to changes in water chemistry than the CNS. Electrophysiology, histology, and transcriptomics were used to explore the effect of exposure to CO2 acidified water on the olfactory epithelium (OE) of the Senegalese sole (Solea senegalensis). The upper and lower OE of this flatfish detect different odorants and are in contact with different environments. Acute exposure to acidified water decreased olfactory sensitivity more in the upper than in the lower OE. After chronic exposure to high CO2 there was no histological changes in the upper OE, however, in the lower OE, there was a massive infiltration of melanomacrophage (MMC) and tissue disorganization. In addition, in the upper OE, differential expressed gene transcripts (DETs) were related to inflammation and innate immune processes whereas in the lower OE, DETs were related to the adaptative immune response. Differential regulation of genes related to neurogenesis and plasticity occurred in both epithelia.

The effects of ocean acidification in sole OE depends on the nostril, however the occurrence of an exacerbated immune response, OE remodelling and reduced sensitivity indicate that ocean acidification is likely to have significant and unpredictable consequences for behaviour.

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Short-term negative effects of seawater acidification on the rhodolith holobionts metatranscriptome

Published 7 February 2025 Science Closed
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Highlights

  • Cyanobacteria dominate the microbial community in living rhodoliths.
  • Vibrionales dominate dead rhodolith skeletons.
  • Short-term (1 h) acidification affects the microbial community structure.
  • Diverse functional genes modulate microbe-host interactions.

Abstract

Rhodolith holobionts are formed by calcareous coralline algae (e.g., Corallinales) and associated microbiomes. The largest rhodolith bank in the South Atlantic is located in the Abrolhos Bank, in southwestern Brazil, covering an area of 22,000 km2. Rhodoliths serve as nurseries for marine life. However, ocean acidification threatens them with extinction. The acute effects of high pCO₂ levels on rhodolith metatranscriptomes remain unknown. This study investigates the transcriptomic profiles of rhodoliths exposed to short-term (96-h) high pCO₂ levels (up to 1638 ppm). Metatranscriptomes were generated for both dead and alive rhodoliths (15.48 million Illumina reads in total). Alive rhodoliths showed an enrichment of gene transcripts related to environmental stress responses and photosynthesis (Cyanobacteria). In contrast, the metatranscriptomes of dead rhodoliths were dominated by heterotrophic (Proteobacteria and Bacteroidetes) metabolism and virulence factors. The rhodolith holobiont metatranscriptomes respond rapidly to short-term acidification (within 1 h), suggesting that these holobionts may have some capacity to cope with acute acidification effects. However, the negative impacts of prolonged ocean acidification on rhodolith health cannot be overlooked. Rhodoliths exposed to low pH (7.5) for 96 h exhibited a completely altered transcriptomic profile compared to controls. This study highlights the plasticity of rhodolith transcriptomes in the face of ocean acidification and climate change.

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Proteomics analysis reveals the antagonistic interaction between high CO2 and warming in the adaptation of the marine diatom Thalassiosira weissflogii in future oceans

Published 6 February 2025 Science Closed
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Highlights

  • Central carbon and fatty acid metabolism up-regulated after warming adaptation.
  • High CO2 acted antagonistically with warming to slow down these pathways.
  • Amino acid synthesis accelerated after high CO2 and warming adaptation.

Abstract

While it is known that warming and rising CO2 level might interactively affect the long-term adaptation of marine diatoms, the molecular and physiological mechanisms underlying these interactions in the marine diatom Thalassiosira weissflogii on an evolutionary scale remain largely unexplored. In this study, we investigated the changes in metabolic pathways and physiological responses of T. weissflogii under long-term ocean acidification and/or warming conditions (∼3.5 years), integrating proteomics analyses and physiological measurements. Our findings reveal that proteins involved in central carbon metabolisms (e.g., tricarboxylic acid cycle and glycolysis) and fatty acid metabolism were significantly up-regulated in the long-term warming-adapted populations. However, the long-term adaptation to high CO2 acted antagonistically with warming, slowing down the central carbon metabolism and fatty acid metabolism by down-regulating protein expressions in the key metabolic pathways of the glycolysis and tricarboxylic acid cycle. Additionally, amino acid synthesis was accelerated in the long-term warming and its combination with high CO2-adapted populations. Physiological measurements further supported these findings, showing altered growth rates and metabolic activity under the combined warming and high CO2 conditions. Our results provide new insights into the molecular mechanisms underpinning the antagonistic interaction between high CO2 and warming on marine phytoplankton in the context of global change.

Continue reading ‘Proteomics analysis reveals the antagonistic interaction between high CO2 and warming in the adaptation of the marine diatom Thalassiosira weissflogii in future oceans’

Molecular and physiological responses of black rockfish (Sebastes schlegelii) to short- and medium-term ocean acidification

Published 5 February 2025 Science Closed
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Ocean acidification (OA) is one of the greatest threats to marine species, with widespread impacts on their physiological functions. However, the adaptive capacities of many marine species to OA and the underlying mechanisms remain unclear. In this study, we investigated the effects of short-term (4 days) and medium-term (30 days) CO2 exposure (pH 8.0, 7.6, and 7.3) on black rockfish (Sebastes schlegelii), focusing on histopathological changes in gill tissues, ion transport biomarkers, oxidative stress indicators, and transcriptomic responses. The results showed that both short-term and medium-term OA induced significant morphological changes in gill tissues, including epithelial lifting, hyperplasia, hypertrophy, and lamellar clubbing, which are likely adaptive mechanisms for maintaining homeostasis. Both Na+/K+-ATPase and carbonic anhydrase (CA) activities increased significantly in both short- and medium-term exposure, while Ca2+-ATPase activity was elevated only in the short-term, suggesting differential enzyme regulation over time to sustain ionic balance. Additionally, oxidative stress indicators (superoxide dismutase (SOD), catalase (CAT), malondialdehyde (MDA), reduced glutathione (GSH) and glutathione peroxidase (GPx)) were significantly elevated after both exposure durations, indicating that the antioxidant defense system was activated. Moreover, the integrated biomarker response (IBR) index further indicated that the stress response was more pronounced during short-term exposure. Transcriptomic analysis reveals significant alterations in pathways related to calcium signaling, cytoskeletal structure, energy metabolism, and oxidative stress following short-term exposure. In contrast, medium-term exposure leads to significant enrichment of pathways associated with cell-environment interactions, highlighting the molecular adaptations of S. schlegelii to OA-induced stress. These findings provide valuable insights into the mechanisms of OA tolerance in S. schlegelii and contribute to understanding the adaptability of marine species in future ocean environments.

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Single-larva RNA sequencing reveals that red sea urchin larvae are vulnerable to co-occurring ocean acidification and hypoxia

Published 22 January 2025 Science Closed
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Anthropogenic carbon dioxide emissions have been increasing rapidly in recent years, driving pH and oxygen levels to record low concentrations in the oceans. Eastern boundary upwelling systems such as the California Current System (CCS) experience exacerbated ocean acidification and hypoxia (OAH) due to the physical and chemical properties of the transported deeper waters. Research efforts have significantly increased in recent years to investigate the deleterious effects of climate change on marine species, but have not focused on the impacts of simultaneous OAH stressor exposure. Additionally, few studies have explored the physiological impacts of these environmental stressors on the earliest life stages, which are more vulnerable and represent natural population bottlenecks in organismal life cycles. The physiological response of the ecologically and commercially important red sea urchin (Mesocentrotus franciscanus) was assessed by exposing larvae to a variety of OAH conditions, mimicking the range of ecologically relevant conditions encountered currently and in the near future along the CCS. Skeleton dissolution, larval development, and gene expression show a response with clearly delineated thresholds that were related to OAH severity. Skeletal dissolution and the induction of Acid-sensing Ion Channel 1A at pH 7.94/5.70 DO mg/L provide particularly sensitive markers of OAH, with dramatic shifts in larval morphology and gene expression detected at the pH/DO transition of 7.71/3.71–7.27/2.72 mg/L. Experimental simulations that describe physiological thresholds and establish molecular markers of OAH exposure will provide fishery management with the tools to predict patterns of larval recruitment and forecast population dynamics.

Continue reading ‘Single-larva RNA sequencing reveals that red sea urchin larvae are vulnerable to co-occurring ocean acidification and hypoxia’

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