Ocean Acidification

Quantifying the threat of ocean acidification to predict its impact on shellfish larvae

1. Key Points

• As ocean acidification worsens, concerns over its effects on calcifying organisms^※1, including shellfish and coral, are increasing. To date, research has been unable to quantify the impact of ocean acidification on calcifying organisms, largely because of their incredibly small shells.
• In the present study, mollusk larvae with tiny shells measuring approximately 0.1 mm were raised in an environment designed to simulate severe ocean acidification. Subsequently, a high-resolution microfocus X-ray computed tomography (MXCT)^※2 scanner was used to obtain three-dimensional measurements of the shells. For the first time, globally, changes in shell morphology, in terms of reduced shell thickness, size, and density, were quantified precisely.
• In addition, gene expression in genomic domains involved in shell formation was reduced significantly, which marks a significant step toward comprehensive understanding of the effects of ocean acidification on organisms, with respect to biological responses and the impact on shells.
• The methodology employed in the present study could also be applied to other organisms with calcified shells or skeletons, such as bivalves and corals. Such studies could facilitate environmental impact assessment, marine conservation, and fisheries resource management in future.

Fig. 1. Predicting the future using a technique to measure the shell density of shellfish larvae.

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2. Overview

As global warming intensifies, so does ocean acidification. Such ocean acidification poses a serious threat to marine ecosystems. It not only lowers the pH of seawater but also reduces the “aragonite saturation state (Ω_aragonaite)^{※3, ※4} ”. Aragonite is a crystalline form of calcium carbonate. When the “aragonite saturation state” is 1 or higher, it indicates a supersaturated state; conversely, values below 1 indicate an unsaturated state. The value is as an indicator of how easily organisms can form aragonite-based shells or skeletons. When the aragonite saturation state decreases, it is more difficult for organisms to form aragonite shells or skeletons. However, evaluating the effects of ocean acidification on early developmental stages of organisms such as plankton and mollusk larvae with aragonite shells, has proven challenging. Their shells are exceptionally small (approximately 0.1 mm in diameter and only a few micrometers^※5 thick), which makes precise quantitative assessment more challenging than with mature specimens.

To address the challenges above, Keisuke Shimizu (Associate Researcher) and Katsunori Kimoto (Acting Group Leader) from the Japan Agency for Marine-Earth Science and Technology Research Institute for Global Change Earth Surface System Research Center, alongside Masahide Wakita (Associate Researcher, Mutsu Research Institute), carried out joint research with Takenori Sasaki (Associate Professor, University Museum at the University of Tokyo). The team analyzed the morphology of the shells of shellfish larvae, using high-resolution MXCT and scanning electron microscopy (SEM)^※6, as well as gene expression. Globally, the research team is the first to successfully visualize and quantify the effects of decreased aragonite saturation on the growth and structure of extremely small shells (approximately 0.1 mm) composed of aragonite crystals, using shell density (which is analogous to human bone density) as a novel growth marker. In addition, the findings suggest that a decrease in aragonite saturation may both directly impact shells and influence gene expression domains involved in shell formation in shellfish larvae. The findings could facilitate prediction of the effects of environmental change (such as global warming and acidification) on calcifying organisms such as shellfish and corals.

These results have been published in the Journal of Molluscan Studies on September 18 (Japan time). The research was conducted with the support of a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (KAKENHI; JP23H02299).

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Une nouvelle limite planétaire a été franchie pour la première fois en 2025: l’acidification des océans. Ce processus, directement lié à nos émissions de CO2, est délétère pour les écosystèmes marins.

L’acidité des océans perturbe la reproduction, la croissance et les fonctions métaboliques de nombreuses espèces. WIKIMEDIA COMMONS

Après celle sur le cycle de l’eau en 2023, une nouvelle limite planétaire a été franchie pour la première fois en 2025: l’acidification des océans. Provoquée par nos émissions de CO2, elle vient de dépasser un seuil alarmant. C’est la conclusion centrale du rapport sur les limites planétaires publié le 24 septembre par le Planetary Boundaries Science Lab, un laboratoire allemand dépendant de l’Institut de recherche de Potsdam sur les effets du changement climatique.

La notion de limites planétaires est développée depuis 2009 par plusieurs scientifiques à la pointe des sciences du «système Terre», autour notamment du chercheur suédois Johan Rockström. Ils définissent ces limites comme autant de seuils dans des processus planétaires à ne pas franchir, au risque de déstabiliser l’ensemble du système de manière irréversible, avec des effets majeurs pour le vivant. L’humanité, entre autres, dépend depuis 12 000 ans de cette stabilité pour «vivre, grandir et prospérer en toute sécurité», répète avec insistance le rapport.

7 limites dépassées sur 9

Les signaux rouges clignotent de toutes parts. Sur neuf limites planétaires identifiées par les chercheurs, l’acidification des océans est la septième à être franchie. Les six premières (changement climatique, cycle de l’eau, biodiversité, perturbations du cycle de l’azote et du phosphore, déforestation et changement d’utilisation des sols, pollution terrestre par des milliers de substances synthétiques) sont non seulement déjà dépassées, mais leur situation continue de s’aggraver.

Seules deux limites sont respectées et ne se détériorent pas: la pollution aux aérosols atmosphériques et le maintien de la couche d’ozone.

L’acidité de l’eau à la surface de l’océan a augmenté de 30 à 40% depuis l’ère préindustrielle, alertent les auteurs du rapport. Un processus directement lié à nos émissions de gaz à effet de serre puisque l’océan a la capacité de dissoudre une partie du CO2 atmosphérique. Il est même un puits de carbone essentiel, qui absorbe environ le quart de l’ensemble des émissions anthropiques.

Revers de la médaille: ce CO2 dissout dans l’eau conduit, par une suite de réactions chimiques, à augmenter l’acidité de l’océan. Un phénomène extrêmement délétère pour les organismes marins. Beaucoup d’espèces – coraux, mollusques et certains crustacés notamment – ont de plus en plus de difficulté à fabriquer leur coquille et leur squelette lorsque l’acidité augmente.

Working from a dock on St. Helena Island, S.C., on a sweltering day this summer, Ed Atkins pulled in a five-foot cast net from the water and dumped out a few glossy white shrimp from the salt marsh.

Mr. Atkins, a Gullah Geechee fisherman, sells live bait to anglers in a shop his parents opened in 1957. “When they passed, they made sure I tapped into it and keep it going,” he said. “I’ve been doing it myself now for 40 years.”

These marshes, which underpin Mr. Atkins’s way of life, are where the line between land and sea blurs. They provide a crucial nursery habitat for many marine species, including commercial and recreational fisheries.

But these vast, seemingly timeless seascapes have become some of the world’s most vulnerable marine habitats, according to a new study published on Thursday in the journal Science that adds up and maps the ways human activity is profoundly reshaping oceans and coastlines around the world.

Soon, many of Earth’s marine ecosystems could be fundamentally and forever altered if pressures like climate change, overfishing, ocean acidification and coastal development continue unabated, according to the authors.

© FERNANDO FRAZÃO/AGÊNCIA BRASIL

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A combination of three phenomena is increasingly threatening ecosystems in the southern and equatorial regions of the Atlantic ocean—marine heat waves, high acidification, and low chlorophyll concentration.

Before 2016, it was unusual for these factors to converge. Since then, they have been observed simultaneously every year. All three phenomena stem from the current climate emergency.

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The increased occurrence of these three drivers makes it impossible for ecosystems to recover, as a minimum amount of time is required for regeneration to take place.

The study

The study was published in the journal Nature Communications and was carried out by researchers from the Federal University of Santa Catarina (UFSC) and the National Institute for Ocean Research (INPO).

The data cover 1999 through 2018 and were collected using research satellites. Six regions of the South Atlantic were evaluated, considering their high biodiversity and biological productivity.

The locations studied are the Western Equatorial Atlantic (near the coast of the Brazilian Northeast), the Western Subtropical Atlantic, the Brazil-Malvinas Confluence, the Gulf of Guinea, the Angola Front, and the Agulhas Current (which connects the Atlantic and Indian Oceans).

An international team of researchers, led by a geologist at the University of Greifswald has investigated unusually well-preserved fossils of reef corals from the subtropical Central Paratethys Sea to analyse their ability to withstand ocean warming and acidification during the Middle Miocene approximately 16 to 13 million years ago. This period was characterised by raised levels of carbon dioxide in the atmosphere and a globally warmer climate – similar to scenarios that are expected in the future of our planet.

The researchers from the Universities of Greifswald, Leipzig, and Mainz, as well as the National Autonomous University of Mexico, used seasonal geochemical and growth records to reconstruct how the fossil corals responded to environmental changes during the Middle Miocene. They presented their results in a scientific article recently published in Communications Earth & Environment. The corals could actively regulate the pH value and the saturation level of their internal calcifying fluid. Thus they had a mechanism that helped them to withstand adverse environmental conditions. However, this physiological adaptation did not enable them to compensate the unfavourable conditions in full: “The corals had an extremely low growth rate and their skeletons were only weakly calcified. We assume that this had a considerable impact on the development of reef structures,” explains Dr. Markus Reuter, Research Associate in the field of palaeontology at the University of Greifswald and lead author of the study.

As global climate change intensifies, ocean acidification is becoming a ‘relentless killer’ threatening coral reef ecosystems. Recently, a research paper published in the international authoritative journal Research has revealed diverse survival strategies of reef-building corals in response to ocean acidification, providing a new perspective for understanding and protecting this fragile marine ecosystem.

Since the Industrial Revolution of the Anthropocene, human activities have led to a continuous decline in global ocean pH levels. According to predictions, by the end of this century, the global average seawater pH may drop from 8.0–8.2 to 7.6–7.8, posing a lethal survival crisis for marine organisms that rely on calcium carbonate skeleton systems, especially reef-building corals. While existing research has confirmed that ocean acidification reduces skeletal density and growth rates of reef-building corals, there have been no reports on the survival strategies of different coral species in response to acidified marine environments, particularly the precise dynamic changes of their internal skeleton and canal structures.

To explore these issues in depth, the research team simulated an acidified marine environment with pH values of 7.6–7.8 in the laboratory. They selected four species of reef-building corals widely distributed in the Indo-Pacific region: Acropora muricata, Pocillopora damicornis, Montipora capricornis, and Montipora foliosa. Using high-resolution micro-computed tomography (micro-CT), scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), and transcriptome sequencing (RNA-seq) detection technologies, the researchers conducted multidimensional integrated analysis of the skeletal erosion process, elemental dynamic changes, and gene expression states of these reef-building corals under acidified marine environments.

Species-Specific Survival Strategies

The results suggest that different reef-building coral species have diverse growing strategies in lower pH conditions. A. muricata demonstrated its unique ‘cavity-like’ acid erosion strategy, while the other three species developed degradation characteristics similar to ‘osteoporosis’ in human aging processes, exhibiting disordered skeletal structures, insufficient synthesis of adhesion proteins, and low bone mass, correspondingly.

In a surprising twist for marine science, researchers have discovered that copepods—tiny but crucial creatures at the base of the ocean food chain—use not one but two molecular toolkits to survive in a warming, acidifying ocean.

The discovery reveals a two-pronged strategy: one genetic, the other epigenetic, that helps these animals rapidly adjust and evolve across generations.

The findings, published July 15 in Proceedings of the National Academy of Sciences, offer a rare dose of optimism in climate research. Led by Melissa Pespeni at the University of Vermont, the study tracked 25 generations of marine copepods under simulated future ocean conditions. The result? Clear evidence that these organisms are not just adapting genetically over time, but also deploying rapid, reversible changes through epigenetic modifications—chemical tags on DNA that influence which genes get expressed.

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The team raised populations of Acartia tonsa—a globally abundant copepod species—in lab conditions mimicking ocean warming, acidification, and their combination. Over one year and 25 generations, researchers measured everything from egg production to genome-level changes. Using cutting-edge sequencing, they tracked:

• Genetic adaptation (DNA sequence changes)
• Epigenetic variation (DNA methylation)
• Gene expression patterns (which genes were turned on or off)

What they found was startling: genetic and epigenetic changes occurred in different regions of the genome and seemed to operate independently. Yet both mechanisms contributed to the copepods’ ability to tolerate stressful environments.

The resistance or vulnerability of marine organisms’ shells to ocean acidification does not depend only on the type of mineral they are made of, as previously thought, but also on factors such as their microstructure and organic content. This is the main conclusion of a study by the ICTA-UAB, which calls for a reassessment of current scientific models.

Ocean acidification — driven by increasing atmospheric CO₂ — has become a critical threat to marine life, particularly for organisms that build calcium carbonate shells. For years, it has been widely assumed that organisms with aragonitic shells (a more soluble form of Calcium carbonate CaCO₃) are more vulnerable than those with shells made of calcite (a less soluble form). However, this assumption was based on the behaviour of synthetic monocrystals produced in inorganic precipitation experiments. Calcium carbonate shells, by contrast, are highly complex structures containing organic material as well as minerals. A new study reveals a far more complex reality challenging oversimplified assumptions based synthetic monocrystals

The research shows that the vulnerability of these organisms cannot be predicted based solely on the mineralogy of their shells. Instead, other factors — such as the shell’s microstructure and organic content — are also critical for understanding how these structures respond to undersaturated and corrosive conditions.

“We have a generalized idea about the impact of ocean acidification on marine shells, but it’s not enough to know whether they’re made of aragonite or calcite. It also matters how they’re built,” explains Gerald Langer, ICTA-UAB researcher and lead author of the study. The way organisms build their shells — including internal structure and organic matter — varies between species and can significantly influence their resistance to more acidic seawater.

The experimental evidence analyzed by the team includes cases where structures made of the same mineral exhibit very different dissolution behaviours, depending on their internal design or the presence of organic coatings. A paradigmatic example is that of coccolithophores, where the same species shows variable shell resistance depending on its life cycle stage, even though all phases use the same type of calcium carbonate.

This finding has important implications for conservation policies and for scientific models predicting the impacts of climate change on marine biodiversity. Many of these models use mineralogy as a direct proxy for vulnerability — a practice that, according to this new research, needs to be fundamentally re-evaluated.

“This study challenges one of the foundations of relevant scientific assessments used by international bodies, by showing that mineralogy alone does not predict the resilience of calcifying species in acidifying oceans,” says Patrizia Ziveri, ICTA-UAB research professor and co-author of the study. ““As oceans continue acidifying, improving our understanding of which species are most at risk is essential for designing effective protection strategies,” Ziveri adds.

“The signs of the ocean in distress are all around us”, said Peter Thomson, Special Envoy of the Secretary-General of the United Nations for the Ocean, at the conference in Nice, France last week. “The time of debating with the denialists is over”. This statement of intent backed a slew of agreements that aim to remedy the damage already done to our oceans and prevent further harm. Overfishing, deep-sea mining, pollution with a focus on plastic, with acidification and other threats associated with climate change were on the agenda of global problems to eliminate. We all knew these problems were bad and getting worse, but a new report reveals that we continue to race past critical tipping points without even realizing it.

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When carbon dioxide is released into the atmosphere about 25% of it will end up in the oceans where it dissolves, and makes the water more acidic. This change in pH is as drastic a change in the environment as temperature or any other abiotic factor. This new aquatic chemistry isn’t something to which organisms can adapt, and they’re correspondingly suffering. Comparing certain species of shellfish with their pre-Industrial Revolution conspecifics (members of the same species) collected in 1875 by the crew of the HMS Challenger, we see that they’re up to 76% thinner than their ancestors. This was observed with a 40% increase in acidity. By 2100 the oceans will be 150% more acidic than at present.

This “Evil Twin” of Climate Change has been underestimated. We’re realizing that we’ve crossed a significant tipping point five years ago. Ocean Acidification is so dramatic that shellfish larvae can’t form their shells. We now understand that the acidity interferes with the creation of calcium carbonate that’s need to form the shells of these organisms. Oyster farmers from the Pacific Northwest have observed this since at the early 2000s. Coral, Crabs, and Krill are some of the organisms that have been specifically studied and seen to be struggling. It would be sad in and of itself if we couldn’t enjoy delicious crabs and mussels anymore, but this is worse when we consider that it signals a pending, global ecological catastrophe.

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Why is this happening?

We’ve been abundantly releasing carbon since the Industrial Revolution. Even with man-made global warming being hypothesized in the late 1800s, it’s taken a long time for us to feel its effects. Part of this is because significant amounts of carbon dioxide get absorbed into the oceans, from atmosphere to ocean surface, removing its warming potential. The oceans are so vast that as of 2010 they were storing about 16 times as much of carbon as makes up all living plants and animals on earth. This quantity is 60 times the amount that was in the atmosphere before the Industrial Revolution.

The oceans will have a saturation point at which they can’t absorb more carbon. That can be a concern eventually but don’t worry, that won’t happen until about a pH of 7.5. The majority of marine life will be dead by then. How serious of a problem is this? How likely are we to reach levels where even our biggest carbon reserve can’t take it anymore? If not likely any time soon, it’s a real enough of a question that scientists are proposing a new indicator to quantify ocean acidification.

Gamma Subscript CO2

In this paper published in May of this year, scientists propose a new variable (γ_CO2) to represent the absorption potential of the oceans. This is needed because as stated, we have pumped so much carbon into the atmosphere, which in turn absorbs into the oceans, that we need new math to do future calculations. Without modifying our current trajectory, we could reach a pH of 7.8 by 2100, which would be comparable to 14-17 million years ago when our planet was in the midst of an extinction event.

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At the dawn of the millennium, a group of eminent scientists began compiling a list of the threats they felt were most likely to impact the world’s rocky shorelines over the coming quarter of a century.

Published in 2002, it included forecasts that – among other things – pollution from oil spills would decrease, the number of invasive species across the world would rise, genetically-modified organisms would have harmful effects on the ocean, and the impacts of global climate change would be felt more intensely.

Now, 25 years on, the same academics – along with a larger and more wide-ranging team of international experts – have revisited their forecasts and discovered that many of them were correct, either in whole or in part, while others haven’t had the impacts that were envisaged at the time.

They have also charted some of the other threats to have emerged and grown in significance since their original work, with notable examples including global plastic pollution, ocean acidification, extreme storms and weather, and light and noise pollution.

In doing so, they have also highlighted that while there are key issues they believe are likely to threaten the world’s coastlines between now and 2050, others may also emerge that require varying levels of local and global action to try and tackle them.

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What the scientists missed

• The impacts of coastal mining;
• Ocean acidification and its potential impact on marine species;
• The effects of artificial light pollution;
• The effects of noise pollution;
• Extreme flood and drought events;
• The scale and effects of plastic pollution;
• The impacts of pharmaceutical contamination;
• The combined effects of various environmental threats and chemical compounds.

The full study – Hawkins et al: Hindsight informs foresight: revisiting millennial forecasts of impacts and status of rocky shores in 2025 – is published in Marine Pollution Bulletin, DOI: 10.1016/j.marpolbul.2025.118214.