The potential impacts of climate change on marine habitats were assessed using RCP4.5 and RCP8.5 projections of environmental parameters that included sea surface temperature (SST), pH, salinity, planktonic productivity (PP) and current strength (CS). The analysis was conducted separately for three distinct oceanographic regions of the Portuguese coastline (North, Centre and South) up to the middle of the century. Temporal trends in environmental variables were assessed using time series analyses. Overall, changes expected up to the middle of the century include increasing SST and PP, decreasing pH and salinity, and slight increases in CS. Spatial–temporal analyses revealed high present–future environmental overlay for most environmental variables. However, changes in individual environmental variables cumulatively resulted in statistically significant changes in environmental similarity. Still, the projected changes are not expected to exceed ecological thresholds, above which they would be likely to alter species’ habitat suitability or to result in species distribution shifts. Anomaly analyses suggest that present–future shifts do not surpass 1/5 (pH, PP, CS) or 2/3 (salinity) of the unit, regardless of projection and area, while SST anomalies ranged from −1.1 °C to 1.1 °C. Compared to IPCC large-scale predictions for Atlantic/Mediterranean regions, the intensity of shifts on the Portuguese coast may be lower.
Continue reading ‘Impact of climate change on Portuguese marine coastal environments’Posts Tagged 'modeling'
Impact of climate change on Portuguese marine coastal environments
Published 9 July 2026 Science Leave a CommentTags: chemistry, modeling, regionalmodeling, review
Study on the mechanical characteristics of the stress relaxation in the carbonate rock after high-temperature acidification
Published 3 July 2026 Science Leave a CommentTags: chemistry, laboratory, modeling, paleo
To elucidate the mechanism by which acidification influences wellbore stability in deep reservoir formations, this study investigates the rheological and mechanical behaviors of the carbonate rock subjected to high-temperature acid etching. A novel experimental system was developed to characterize the stress relaxation behavior of the acid-etched carbonate rock, and the characteristics of the stress relaxation curves under various acid etching conditions and strain levels were systematically analyzed. Combined with Burgers model and the Levenberg–Marquardt algorithm, the evolution of rheological parameters of the carbonate rock under different acid etching regimes was quantitatively evaluated. The results indicate that the acid-etched carbonate rock exhibit significant rheological mechanical properties due to the presence of developed microcracks and complex pore structures. Under the identical acid etching duration and temperature, the initial stress, residual stress, and time required for stress relaxation stabilization all increase with increasing the strain level. Overall, the stress relaxation magnitude prior to the core fracture ranges from 15 to 25 MPa, and the stabilization time for the core stress relaxation falls between 5 and 7 h. The stress relaxation behavior of the acid-etched carbonate core is well described by the Burgers model. At fixed strain levels and temperatures, the instantaneous shear modulus decreases linearly with extended acid etching time, whereas the instantaneous shear modulus and the viscosity coefficients and exhibit exponential degradation. The final variation ranges of the key rheological parameters are determined as follows: instantaneous shear modulus ranges from 5 × 103 to 2 × 104 MPa, instantaneous shear modulus ranges from 6 × 105 to 2 × 106 MPa, viscosity coefficient ranges from 2 × 107 to 8 × 107 MPa h, and viscosity coefficient ranges from 1 × 105 to 1.2 × 106 MPa h. Furthermore, the evolutionary equations correlating the global model fitting parameters with the porosity of acid-etched samples are established, using acid etching time as an intermediate variable. The results of this study provide a theoretical basis for the analysis of wellbore stability after acidification and the selection of acid fracturing completion methods of deep reservoirs.
Continue reading ‘Study on the mechanical characteristics of the stress relaxation in the carbonate rock after high-temperature acidification’Assessing early oil industry awareness of the impacts of fossil fuels on coral reefs using a novel AI agent
Published 3 July 2026 Science Leave a CommentTags: biological response, corals, modeling, review
Global warming threatens to eradicate Earth’s tropical corals. As legal interventions addressing climate change expand, fossil fuel companies’ historical awareness of their products’ damaging effects is increasingly important. We searched historical documents using a large-language-model-based agent, finding that carbon majors were aware by the 1980s of prospective impacts of fossil fuels on corals from ocean acidification, marine heatwaves, sea-level rise, and intensified storms and later funded efforts downplaying such impacts.
Introduction
The world’s tropical coral reefs are under imminent threat of collapse from global warming. Living corals have declined by approximately 50% worldwide since the 1990s, with global warming now the greatest threat to future survival1. Global warming kills corals primarily through increased ocean temperatures and more frequent and intense marine heatwaves, which cause coral bleaching (loss of coral symbionts), exacerbated by ocean acidification (from increased carbon dioxide levels), which weakens coral health, and intensified storms (from increased sea surface temperatures), which physically destroy coral assemblages, all ultimately caused by fossil fuels1. Approximately one billion people worldwide depend directly on coral reefs for livelihoods, food security, and protection from storms and coastal erosion, and coral reefs provide shelter and nourishment to over 30% of the world’s named marine species2. Economically, coral reefs provide an estimated 10 trillion USD per year in ecosystem services, including tens of billions of dollars per year in coral reef tourism3, and potential efforts to restore reefs lost over the last decade alone have been estimated to cost around 1 trillion USD2. Mass coral bleaching and mortality from marine heatwaves driven by global warming is ongoing4. The Intergovernmental Panel on Climate Change (IPCC) predicts mortality of 70—90% of the world’s reef-building corals at global warming of 1.5 °C and mortality of more than 99% at 2 °C1.
Legal interventions may play a critical role in helping to protect the world’s coral reefs and associated ecosystems (for example, by securing funding for reef monitoring and rehabilitation) and in compensating affected communities for economic losses associated with climate-change-driven coral impacts. In this context, the history of fossil fuel industry awareness of the foreseeable impacts of climate change on coral reefs is highly relevant. Climate lawsuits against governments, fossil fuel producers, and other parties have expanded in number and sophistication over the past decade5 and have recently cited impacts on coral reefs6. Additionally, the 2024 and 2025 advisory opinions from the International Tribunal for the Law of the Sea (ITLOS)7 and the International Court of Justice (ICJ)8 on climate change clarified, respectively, that greenhouse gases are marine pollutants under the United Nations Convention on the Law of the Sea (UNCLOS) and that best efforts to attain the 1.5 °C warming limit of the United Nations Framework Convention on Climate Change (UNFCCC) Paris Agreement are legally binding on governments under international law, strengthening the basis for legal actions seeking to mitigate global warming and obtain reparations for damages. Research on the fossil fuel industry’s internal knowledge of global warming9, public-facing denial and minimization of the problem10,11, and false assurances to be solving it12 has clarified global warming as not only a scientific and technological problem but also one of corporate corruption subject to legal correction and remedy13. Such research has so far informed dozens of ongoing legal actions seeking industry accountability for climate change14.
Continue reading ‘Assessing early oil industry awareness of the impacts of fossil fuels on coral reefs using a novel AI agent’Erosion-driven delayed warming and marine stress prior to the end-Permian mass extinction
Published 30 June 2026 Science ClosedTags: modeling, paleo, regionalmodeling
The end-Permian mass extinction (EPME) presents an anomaly: intense global warming lags the onset of the carbon isotope excursion (CIE) by ~50,000 years, challenging the presumed link between carbon cycle perturbations and climate warming. Using biogeochemical modeling, Bayesian inversion, and multiple proxies, here we show that incorporating continental erosion as a forcing term into the hyperthermal models can resolve this decoupling. Enhanced erosion, likely resulting from the terrestrial die-off of vegetation, accelerates continental weathering, which buffers early carbon release and delays global warming. This process also increases riverine phosphorus export to the oceans, fostering gradual marine anoxia and preconditioning the oceans for the extinction event. With these findings, we present a coherent unifying scenario for the EPME environmental dynamics. Furthermore, our study refines the hyperthermal paradigm, offering implications for future climate scenarios.
Continue reading ‘Erosion-driven delayed warming and marine stress prior to the end-Permian mass extinction’Will the Mediterranean sea be a cul-de-sac for marine gastropods under climate change?
Published 23 June 2026 Science ClosedTags: biological response, BRcommunity, communitymodeling, individualmodeling, Mediterranean, modeling, mollusks, North Atlantic, physiology, reproduction
Marine ecosystems are undergoing rapid transformation under climate change, yet the responses of many marine invertebrates remain vastly understudied. In particular, for many benthic gastropods there is a striking imbalance between their traditional appreciation by shell collectors—and, consequently, their consistent representation in Natural History Collections—and the limited attention they receive in ecological and conservation studies. Focusing on the northeastern Atlantic and the Mediterranean, the cowries Luria lurida, Naria spurca, Zonaria pyrum and the frog-shell Talisman scrobilator are emblematic examples of this knowledge gap, despite being frequently mentioned as species of conservation concern. Using long-term occurrence records spanning more than a century, we modelled past and present distributions of these species and explored their potential responses to future climate scenarios through a multi-temporal Species Distribution Modelling framework. Our results show that intermediate climatic conditions—both in time (2050–2060 vs. 2090–2100) and scenario intensity (moderate SSP2-4.5 versus high-emission SSP5-8.5)—may represent a critical transition phase, leading to habitat contractions without compensatory gains in newly emerging suitable areas. The Mediterranean Sea is expected to increasingly function as a cul-de-sac, with the dominant circulation patterns strongly limiting outward movements towards cooler regions for species relying on planktic larvae for dispersal. Furthermore, incorporating larval sensitivity to reduced pH suggests that large areas of the Atlantic Ocean may actually result unsuitable for larval persistence, substantially reducing the habitat effectively available for completion of the full life cycle; this highlights the need to account for connectivity, life-history constraints and juvenile-stage sensitivity when assessing climate-driven range shifts in shelled organisms with planktic larvae.
Continue reading ‘Will the Mediterranean sea be a cul-de-sac for marine gastropods under climate change?’A basin-wide assessment of pH changes in the Mediterranean Sea based on reanalysis products
Published 19 June 2026 Science ClosedTags: biogeochemistry, chemistry, Mediterranean, modeling, regionalmodeling
Ocean acidification, driven by increasing atmospheric CO2 concentrations, poses a growing threat to marine ecosystems and biogeochemical processes. The Mediterranean Sea, characterized by complex circulation patterns and distinct hydrographic sub-basins, represents a sensitive region for assessing basin-scale pH variability. However, long-term in situ pH observations remain spatially sparse and unevenly distributed, limiting the assessment of coherent spatiotemporal trends across the basin. Here, we present a basin-wide spatiotemporal assessment of pH trends in the Mediterranean using an 18-year biogeochemical reanalysis dataset from the Copernicus Marine Environment Monitoring Service. Our analysis reveals a consistent vertical structuring of pH trends, with negative trends in surface waters and contrasting, often neutral to weakly positive tendencies at depth. The magnitude and vertical extent of these trends vary regionally and are closely linked to local circulation regimes, water-mass formation processes, and remineralization dynamics. In deep-water formation regions such as the Adriatic, Ionian, and Aegean Seas, negative pH trends extend throughout much of the water column, whereas in the Levantine Basin, mesoscale circulation structures confine pH changes primarily to a relatively thin surface layer. These results demonstrate that basin-scale analyses based on high-quality, publicly accessible biogeochemical reanalysis products, such as CMEMS, can provide a spatially integrated perspective on long-term pH variability, complementing existing observational records by bridging spatial and temporal gaps. The framework presented here offers a reproducible approach for systematically assessing depth and region resolved pH trends.
Continue reading ‘A basin-wide assessment of pH changes in the Mediterranean Sea based on reanalysis products’Dialogue, inclusion, and adaptation in a remote marine sanctuary: evidence from Flower Garden Banks
Published 10 June 2026 Science ClosedTags: modeling, policy, review
Interdisciplinary, stakeholder-engaged research is increasingly being used for managing climate change in social-ecological systems. We apply a Collaborative Adaptive Experimental Governance lens to the Flower Garden Banks National Marine Sanctuary, a remote, relatively pristine coral reef system ~130–190 km offshore in the Gulf of Mexico, where biodiversity protection coexists with recreation and offshore energy. We coupled participatory social science with climate and ecosystem modeling to inform dialogue with decision-makers and users. First, we generated scenarios using Community Earth System Model2-LE ocean temperature and aragonite saturation state to characterize warming and acidification; translated heat stress into a variability-based coral bleaching index; and projected demersal and pelagic fish biomass. We then conducted 37 semi-structured interviews (managers, oil and gas, commercial and recreational fisheries, dive operators, Non-governmental organizations, and science/education), employed multi-coder reliability, and triangulated findings with policy and legal documents. Results highlight the centrality of the Sanctuary Advisory Council in structuring inclusive dialogue, co-producing recommendations, and supporting outreach in distant coastal communities. Multi-level coordination among NOAA, the Gulf of Mexico Fishery Management Council, and the Bureau of Ocean Energy Management enabled boundary expansion and reconciled conservation with industry and fishing interests. Key barriers to adaptive responses include offshore remoteness and logistics, limited public awareness, funding constraints, trust deficits, and procedural delays; pressures that intersect with warming, acidification, and episodic hypoxia. Our study shows that remote marine protected areas can operationalize inclusive, experimental governance to align science and management, but sustained investment in monitoring, restoration capacity, boundary-spanning outreach, and cross-agency coordination is needed.
Continue reading ‘Dialogue, inclusion, and adaptation in a remote marine sanctuary: evidence from Flower Garden Banks’Seasonal upwelling shapes coral reef community structure and photophysiology on the Pacific Coast of Costa Rica
Published 3 June 2026 Science ClosedTags: algae, biological response, community composition, corals, echinoderms, field, modeling, North Pacific, otherprocess, photosynthesis, physiology, regionalmodeling
Reef-building corals form the calcium-carbonate frameworks that underpin tropical coral reefs, yet global coral cover has declined by ~50% in recent decades, due to marine heatwaves and other stressors. Identifying refugia environments, such as upwelling systems, that buffer stress, promote recovery, and enhance resilience by promoting physiological plasticity that supports thermotolerance is therefore critical. Here, we compared benthic community composition, coral percent cover, and photo-physiology between an upwelling location in the Gulf of Papagayo and a non-upwelling location in Sámara on the Pacific coast of Costa Rica. Waters in Papagayo were cooler, more acidic, and richer in chlorophyll a. Reefs at this location exhibited higher crustose coralline algae, higher sea urchin cover, and lower macroalgae cover, compared to Sámara. Papagayo also showed higher stony coral cover, driven by Pocillopora spp., while Sámara was dominated by massive, heat-tolerant Porites spp.. When significant, photophysiological measurements showed 9.7 – 44.5% higher photosynthetic efficiency (Fv’/Fm’) in Papagayo corals and 19.94 – 42.75 % higher maximum photosynthetic rates (Pmax) in Sámara corals. These results highlight how contrasting environmental regimes within a relatively small geographic area can shape distinct coral community compositions and photophysiological strategies, with implications for identifying areas of reef persistence or refugia.
Continue reading ‘Seasonal upwelling shapes coral reef community structure and photophysiology on the Pacific Coast of Costa Rica’Upper-ocean variability of the marine carbonate system in the Northeast Pacific
Published 2 June 2026 Science ClosedTags: chemistry, field, globalmodeling, modeling, North Pacific, regionalmodeling
In the Northeast Pacific, the marine carbonate system’s variability across timescales is not well constrained. Here, we quantify observed seasonal and non-seasonal variability in Dissolved Inorganic Carbon (DIC), partial pressure of carbon dioxide () and aragonite saturation state and discuss potential drivers. We used three decades of observations from four Line P time series stations, the longest marine carbonate system time series in the Northeast Pacific (1990–2019). To gauge the spatial extent of the variability patterns, we used output from a global ocean model representing the observed period. In the Northeast Pacific, seasonal and non-seasonal variability at 10 m was minimal, mostly damped by the opposing influence of DIC and temperature changes at both seasonal and interannual timescales. For DIC and , the seasonal cycle dominated total variability in the top 60–70 m, with mean-transect 10 m seasonal amplitudes of 35 3 μmol and 0.31 0.04, respectively. In the upper 60–70 m, the magnitude of non-seasonal variability was at least half that of the seasonal variability for most variables. From five climate indices examined, we focused on the basin-scale Pacific Decadal Oscillation index (PDO) to investigate potential drivers of non-seasonal variability, with 20%–40% of the non-seasonal variability in DIC and associated to this index. In the Northeast Pacific, positive PDO periods were linked to a mean reduction in 10 m DIC of 5 μmol and an increase in 10 m of 0.04 for each PDO unit increase, which could potentially reduce the occurrence and severity of ocean acidification events. The opposite could be expected during negative PDO periods.
Plain Language Summary
Using 30 years of observations from the Northeast Pacific, we characterized sources of variability for three marine carbonate system variables: , dissolved inorganic carbon (DIC) and the saturation state of aragonite (an common indicator of ocean acidification). The seasonal and non-seasonal variability was minimal in the top 10 m. The seasonal cycle of DIC and aragonite saturation state was the major contributor to total variability in the top 60–70 m, and not detectable below. Also, in the top 70 m of the water column, up to 20%–40% of the DIC and aragonite saturation state non-seasonal variability was associated to the Pacific Decadal Oscillation index (PDO). The PDO is a statistics-derived index that captures variability patterns influencing the whole Pacific basin and has a positive and negative phase. We found that a warmer than usual upper water column in the Northeast Pacific during a positive PDO phase, potentially driven by reduced mixing, was linked to a lower DIC and higher values of aragonite saturation state. The opposite could be expected during negative PDO periods. Knowing the magnitude of natural variability in the marine carbonate system is important to identify the emergence of ocean acidification and other human-driven changes in the ocean.
Continue reading ‘Upper-ocean variability of the marine carbonate system in the Northeast Pacific’Hydrodynamic control of coral metabolism: a coupled modeling approach linking flow, physiology, and reef-scale biogeochemistry
Published 2 June 2026 Science ClosedTags: biogeochemistry, biological response, chemistry, community composition, corals, individualmodeling, modeling, otherprocess, physiology, South Pacific
Tropical coral reefs exhibit high variability in coral metabolism, driven by complex interactions among physical, chemical, and biological processes. Understanding the spatiotemporal patterns of coral metabolism and their drivers is critical, as such variability may underpin corals’ adaptive capacity to withstand a warming and acidifying ocean. Here, we use a coupled hydrodynamic–biogeochemical–physiological model to investigate spatial and diel variations in coral metabolic processes (photosynthesis, respiration, and calcification) across Moorea’s north shore reef system under three prevailing wave regimes. We find that photosynthesis varies little across the reef, whereas respiration and calcification show pronounced spatial heterogeneity. These spatial patterns closely mirror the ones in seawater carbonate chemistry and depend strongly on wave-driven flow. Hydrodynamics regulate diffusive exchanges between coral tissues and surrounding seawater, and eventually generate distinct internal chemical environments (in the coelenteron and calcifying fluid) across the reef. Landward reef regions exhibit the greatest spatial and diel variability in coral metabolism. Low-wave, slow-flow conditions amplify metabolic fluctuations throughout the reef, but more strongly in the landward regions. Overall, our results highlight how interactions among transport processes, carbonate chemistry, and coral physiology produce strong day-night fluctuations and spatially heterogeneous but structured metabolic patterns across the reef, which vary systematically with wave conditions.
Continue reading ‘Hydrodynamic control of coral metabolism: a coupled modeling approach linking flow, physiology, and reef-scale biogeochemistry’Darkness and body size shaped end-Cretaceous marine extinction patterns
Published 29 May 2026 Science ClosedTags: communitymodeling, modeling, paleo, phytoplankton
The Chicxulub asteroid impact at the Cretaceous–Paleogene (K–Pg) boundary (66 Ma) is thought to have caused the extinction of around 75% of species in the fossil record by triggering catastrophic environmental changes1. However, despite decades of research, the mechanisms linking the environmental changes to the selective extinction patterns observed in the marine fossil record remain unresolved. Here we use a global trait-based ecosystem model2,3 to establish this causality for the marine plankton community beyond the fossilized groups. Our model simulates diversity dynamics during the initial 100 years after the K–Pg boundary and represents explicitly extinction based on biomass thresholds that scales with body size. Under K–Pg climatic forcings, the model reproduces successfully key observed extinction patterns, including the high vulnerability of planktic foraminifera and other zooplankton, the survival of small mixotrophs4 and phytoplankton5,6, and potential for reduced diversity loss in high-latitude settings7. Our analysis suggests that impact-driven darkness and body-size-dependent extinction thresholds drove most of the observed extinction patterns. These results suggest that plankton ecologies enhance survival through differences in energy demand and acquisition. Our study bridges the gap between fossil evidence of extinction patterns and the K–Pg impact winter hypothesis, highlighting the value of trait-based models for understanding past biodiversity crises.
Continue reading ‘Darkness and body size shaped end-Cretaceous marine extinction patterns’Long term variability of temperature and pH in the Bay of Bengal: an investigation on acoustic perspective
Published 28 May 2026 Science ClosedTags: field, Indian, modeling, regionalmodeling, salinity
This study comprehensively assesses the long-term variability of temperature, ocean acidity changes, and their implications on sound absorption and acoustic propagation in the Bay of Bengal. The analysis reveals a persistent warming trend in the Indian Ocean over the past 50 years, with a significant increase in temperature observed during the Sagar Maitri cruise in 2019. Thermal structure analysis using HadleySST EN4 data indicates warming in the upper 50m but a cooling trend in the 100-200m depth range. Oceanic Heat Content analysis highlights an increasing tendency of heat storage in the upper 50m, indicative of global warming.
In the context of surface ducted propagation, Sonic Layer Depth (SLD) and gradients in the Sound Speed Profile (SSP) were crucial factors influencing acoustic energy behavior. The study revealed a decreasing trend in in-layer gradient (Gr_SL) since 1990, intensifying after that period. The below-layer gradient (Gr_BL) also exhibited a decreasing trend, implying complex dynamics in the sonic layer with potential implications for sound propagation in the surface duct.
The investigation into pH changes spanning 65 years demonstrates a declining trend, particularly since the 1990s, attributed to increased atmospheric CO2 dissolution. The study linked this decrease to anthropogenic activities, aligning with global trends. The analysis of sound absorption illustrated a nonlinear relationship between absorption, frequency, and pH, emphasizing a significant impact of ocean acidification on sound absorption in the Bay of Bengal. The acoustic propagation modeling further highlighted a decrease in transmission loss with reducing pH, leading to increased sound travel and potentially noisier oceans. Salinity variations play a more significant role than temperature in influencing sound absorption.
Continue reading ‘Long term variability of temperature and pH in the Bay of Bengal: an investigation on acoustic perspective’Impacts of ocean acidification and warming (OAW) on abalone growth and reproduction: a dynamic energy budget model approach across SSP scenarios
Published 18 May 2026 Science ClosedTags: biological response, field, individualmodeling, laboratory, modeling, mollusks, morphology, performance, physiology, reproduction
Ocean acidification and warming (OAW) are expected to alter physiology, growth and reproduction of marine ectotherms, yet their combined effects on life-history traits remain unresolved, particularly under poorly defined future food conditions. Using a Dynamic Energy Budget (DEB) model, we investigated how interacting changes in temperature, seawater pH, and food quality may shape somatic growth and reproductive phenology of the European abalone Haliotis tuberculata across four contrasting coastal environments and three Shared Socioeconomic Pathway (SSP) climate scenarios. OAW effects were modeled as increased metabolic maintenance costs, while reduced food quality, driven by OAW, lowered assimilation efficiency, aligning with experimentally-supported limited compensatory feeding.,Our results reveal that warming and food quality strongly drive somatic growth, whit ocean acidification playing a minor role within the modeled range. Food quality remained the primary determinant of maximum body size, while warming amplified growth across all locations, with the largest proportional increases in cooler northern bays. Individuals in the warmest areas remained the largest across scenarios within the model framework. Reproductive timing also shifted consistently, with first spawning occurring markedly earlier under end-of-century conditions, advancing consistently with scenario intensity. Food quality modulated reproductive investment but had weaker effects on the timing of first spawning., These findings highlight that food quality critically mediates organismal responses to OAW and can offset temperature-driven gains in growth and reproduction. By combining expected nutritional constraints with SSP scenarios, our DEB-based approach provide mechanistic insights into the future responses of benthic marine invertebrates to climate change, highlighting the value of these scenario-based projections for better management strategies.
Continue reading ‘Impacts of ocean acidification and warming (OAW) on abalone growth and reproduction: a dynamic energy budget model approach across SSP scenarios’Leveraging AI-driven predictors of enzyme pH optima to unravel microbial adaptation to environmental pH
Published 12 May 2026 Science ClosedTags: chemistry, modeling
It is well-known that pH (potential of hydrogen) influences enzyme catalytic activity (Schomburg and Salzmann, 1991; Nelson et al., 2021). The pH optimum (pHopt), at which an enzyme displays maximal catalytic activity, is therefore critical for enzyme design and applications (Zhang et al., 2025). To identify suitable enzymes for target pH environments or optimize enzymatic performance in biotechnology, enzyme engineering requires efficient characterization of kinetic properties across large numbers of amino acid sequences. However, experimental determination of pHopt for numerous sequences is time-consuming, labor-intensive, and costly. To address these limitations, computational approaches based on machine learning have been developed for rapid prediction of enzyme pHopt, supporting applications in protein engineering.
Recent advances, exemplified by EpHod (enzyme pH optimum prediction with deep learning) (Gado et al., 2025), enable prediction of the enzyme pHopt directly from protein sequences. The EpHod model leverages embeddings from the protein language model (PLM) ESM-1v and achieves a root mean squared error (RMSE) of 1.25 pH units on the held-out test data (Gado et al., 2025). To further improve predictive performance, an increasing number of AI-driven tools have been developed. For instance, (Zhang et al. 2025) introduced the model VENUS-DREAM, which employs the PLM ESM-2 and reduces the RMSE to 0.809. These AI-powered tools are revolutionizing enzyme discovery and design by enabling high-throughput prediction of pHopt.
Similarly, studies of microbial adaptation to environmental pH frequently require knowledge of enzyme pHopt. This information can be used to investigate the underlying adaptive mechanisms. However, experimental determination of pHopt for large-scale enzyme sequences remains impractical due to high costs and low throughput. Fortunately, the high-throughput predictive capacity of these AI-driven tools offers a powerful alternative for obtaining enzyme pHopt values, which can facilitate investigations into the mechanisms by which microorganisms adapt to environmental pH. The potential applications are illustrated with examples below.
Continue reading ‘Leveraging AI-driven predictors of enzyme pH optima to unravel microbial adaptation to environmental pH’Projected future of African marine ecosystems under climate change and stratospheric aerosol injection
Published 8 May 2026 Science ClosedTags: biological response, modeling, multiple factors, North Atlantic, phytoplankton, regionalmodeling, salinity, temperature
Stratospheric Aerosol Injection (SAI) has been proposed as a potential strategy to cool the planet. The ARISE-SAI-1.5 approach, which employes a moderate emission scenario, is simulated to limit future global warming to 1.5°C by injecting aerosols into the stratosphere in the year 2035. However, the climate response to this SAI scenario, particularly along the African coast, remains unclear. In this study, we investigate the potential impacts of climate change under the SSP2-4.5 scenario and ARISE-SAI-1.5 on regional African marine ecosystems through key biological (chlorophyll), physical (salinity, temperature), and chemical (nitrate, acidification, and dissolved oxygen) parameters. Our results indicate that climate change may reduce productivity in African coastal ecosystems, with chlorophyll concentrations decreasing between 10% and 62%. Sea surface temperatures are projected to rise by 1.5°C along the entire coast by 2069, while surface salinity increases up to 0.3 g/kg, except for a slight decrease of up to 0.1 g/kg along the Congolese-Angolan coast. This salinity dipole in the Gulf of Guinea results from enhanced precipitation and river discharge, reinforced by stratification that traps freshwater at the surface. Additionally, climate change drives ocean acidification and may expand the oxygen minimum zone in the Gulf of Guinea, with oxygen levels decreasing by 10%–30% at depths of 100–200 m. Although ARISE-SAI-1.5 may help reduce surface oxygen depletion, it may not significantly mitigate subsurface oxygen loss or continued acidification. Nevertheless, it may reduce some negative climate change impacts on marine ecosystems by stabilizing chlorophyll levels, sea surface temperatures, and salinity.
Plain Language Summary
Stratospheric Aerosol Injection is being explored as a way to cool the planet and limit future global warming, for instance, to 1.5°C in the scenario we explore here (ARISE-SAI-1.5). However, its effects on the ocean, especially along the African coast, are not fully understood. This study examines key factors such as chlorophyll, water temperature, salinity, and oxygen levels to assess changes in marine ecosystems. Our findings show that climate change could reduce productivity, with chlorophyll levels dropping by 10%–62%. Sea surface temperatures are expected to rise by 1.5°C by 2069, and salinity will increase along most coastal areas. The low-oxygen zone in the Gulf of Guinea may expand, making deep waters less habitable for marine life. While the SAI we study here helps slow oxygen loss near the surface, it does not prevent deeper waters from losing oxygen or the ocean from becoming more acidic. However, it can still reduce some harmful effects of climate change by stabilizing chlorophyll levels, temperatures, and salinity.
Continue reading ‘Projected future of African marine ecosystems under climate change and stratospheric aerosol injection’Acidification in coastal waters of Adélie Land, Antarctica (1985–2025)
Published 29 April 2026 Science ClosedTags: Antarctic, chemistry, field, modeling, regionalmodeling, sensor
Ocean acidification is expected to be particularly severe in Antarctic continental shelves due to enhanced anthropogenic carbon uptake in cold waters in response to rising atmospheric CO2, sea-ice retreat, freshening and climate-change feedbacks. Models suggest that undersaturated conditions with respect to aragonite (Ωar), a major form of calcium carbonate formed by marine species, could be reached as soon as 2052 for austral winter. Here we present new ocean carbonate system observations from cruises conducted since 2010 in the Adélie Land coastal region in East Antarctica, along with data from a BCG-Argo float and results from a neural network model for the period 1985–2025. The region is a permanent CO2 sink and was most pronounced since 2006. The CO2 sink leads to a positive increase of surface water total CO2 concentrations (CT) (+0.44 ± 0.01 µmol.kg-1.yr-1) and to a progressive decrease of pH (-0.013 per decade) and Ωar (-0.035 per decade) for the winter season. The lowest surface Ωar of 1.2 was observed in winter 2024 from the float data, a critical limit for some marine species such as pteropod. A projection of the CT concentrations in the future, based on observed anthropogenic CO2 concentrations and emissions scenarios, suggests that aragonite saturation state (Ωar = 1) will occur in surface waters as soon as 2055 in the Adélie Land region, which is part of a larger area of East Antarctica proposed as a Marine Protected Area by the Commission for the Conservation of Antarctic Marine Living Resources since the early 2010s.
Continue reading ‘Acidification in coastal waters of Adélie Land, Antarctica (1985–2025)’Future projections of compound events around the Main Hawaiian Islands
Published 15 April 2026 Science ClosedTags: modeling, North Pacific, regionalmodeling
The consequences of overlapping environmental stressors — referred to as compound events — may be more harmful to marine ecosystems than as individual stressors. Using recently conducted submesoscale-permitting future projections for the Main Hawaiian Islands, we present the first assessment of future compound events for Hawaiian waters. Our analysis focuses on surface and sub-surface heat-stress, ocean acidification, and low-oxygen events and is based on three different greenhouse gas emission scenarios. We show that a large fraction of ocean around Hawai‘i will be subject to compound events in the near future. However, the projected event characteristics such as duration and intensity vary substantially across the region suggesting that potential ecosystem impacts may differ over short distances. Our results reveal that these spatial differences are mainly driven by considerably different magnitudes of natural variability in ocean physics and chemistry across the domain driven by mesoscale processes, while anthropogenic trends exhibit only minor spatial differences. Our analysis demonstrates that small-scale tidal variability can significantly mitigate compound events in near-shore regions including some designated Marine Protected Areas. Overall, our findings highlight the need for high-resolution numerical models as well as for an extended observation network for robust future projections of local extreme events.
Continue reading ‘Future projections of compound events around the Main Hawaiian Islands’Acidification in the Earthʼs oceans: trends and persistence
Published 13 April 2026 Newsletters and reports ClosedTags: chemistry, globalmodeling, modeling
This paper applies fractional integration methods to obtain evidence on ocean acidification, namely the decrease in the pH level in the Earth’s oceans, using the annual Hawaii Ocean Time-series Station ALOHA series as well as the logged one for the period 1985-2024. The chosen modelling framework is more general than standard ones based on the I(0) versus I(1) dichotomy and sheds light on the long memory and persistence properties, as well as on the possible presence of trends, in the pH Level in the Earth’s oceans. The results indicate that the series exhibit a negative and significant time trend; however, whether or not the null hypothesis of a unit root is rejected depends on the assumption made about the errors. The key finding (when the errors are not incorrectly specified as I(0) processes) is the presence of long memory, which implies that the effects of shocks are long-lived, regardless of whether or not mean reversion occurs. Moreover, the recursive analysis indicates that both the degree of persistence and the downward trend in the pH level have increased over time. This evidence points to the urgent need for decisive policies to address the issue of ocean acidification and protect marine life and biodiversity.
Continue reading ‘Acidification in the Earthʼs oceans: trends and persistence’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’An interpretable machine learning approach for alkalinity reconstruction in the Mediterranean Sea
Published 9 April 2026 Science ClosedTags: chemistry, Mediterranean, modeling, regionalmodeling
Highlights
- Genetic Programming provides interpretable alkalinity models for Mediterranean Sea.
- Genetic Programming models capture typical alkalinity patterns and its finer-scale variability.
- Genetic Programming matches or exceeds linear models while remaining interpretable.
- Neural networks yield lowest errors but lack model transparency.
Abstract
Ocean acidification has significant impacts on marine ecosystems and human activities, and its understanding relies on an accurate characterization of the marine carbonate system, in which alkalinity plays a central role.
We propose a Machine Learning (ML) approach based on Genetic Programming (GP) to model alkalinity and apply this framework to the surface layers of the Mediterranean Sea. Our framework produces interpretable equations that capture alkalinity typical patterns and its finer-scale variability by inferring its relation with key physical and biogeochemical variables.
Results, supported by quantitative metrics and visual analyses, demonstrate that our method reliably reproduces the spatio-temporal variability of alkalinity with a high level of predictive accuracy when compared with in situ observations. Moreover, we use the derived alkalinity equations to produce gap-free 2D surface alkalinity maps using satellite data. The maps correctly capture spatial gradients, seasonal patterns, and riverine contributions, reinforcing the robustness of the proposed approach.
Continue reading ‘An interpretable machine learning approach for alkalinity reconstruction in the Mediterranean Sea’
