Ocean Acidification

Globally the ocean absorbs about a quarter of the carbon dioxide produced on land. This varies seasonally and by region. We visit the PAP-SO in spring just as the largest plankton bloom is starting, shown by the orange and red colours in the satellite map below. This productivity makes the northeast Atlantic a key region for carbon dioxide uptake into the ocean.

Satellite image of NE Atlantic chlorophyll.

On JC247 we are using several methods to measure this process. The Met Office ODAS buoy carries instruments for year-round measurement of ocean biogeochemistry, including seawater and atmospheric carbon dioxide (Pro-Oceanus). We observe the phytoplankton bloom at PAP-SO with chlorophyll, oxygen and nutrient sensors that we can compare with satellite images. This year we have an exciting addition to our upper ocean measurements – an underwater holographic camera (LISST-Holo) we can use to measure plankton communities in the surface water. All these measurements help us understand drivers of carbon dioxide uptake.

PAP buoy on deck.

During the research cruise we take physical water samples around the PAP-SO, sampling right down to 4850m depth. The water will be analysed in our laboratories on board, and ashore at NOC. We also have a SubCtech ‘flow through’ system on board. It allows us to map surface seawater carbon dioxide in the whole region around PAP-SO. From the summer of this year a similar system will be fitted permanently to the ship to make measurements during other research cruises and during transit, with the benefit of gathering data in under surveyed regions of the world.

All of the carbon dioxide data we collect on JC247 will contribute to the Surface Ocean CO2 Atlas (SOCAT). This global map of carbon dioxide helps in our understanding of climate change and ocean acidification. PAP data also contributes to the Integrated Carbon Observation System which uses key long-running ocean, land and atmospheric greenhouse gas sites across Europe. We are excited that the PAP-SO has been accepted as a ‘labelled ICOS station’ for carbon dioxide measurements from 2023.

Sue Hartman operating our underway CO2 system.

The team on board the RRS James Cook are grateful to the Met Office for use of the ODAS buoy at PAP-SO as well as all of the technicians, scientists and engineers (both onboard and ashore) who have helped instrument the buoy.

Environmental Sciences Professor Brooke Love and graduate student Rhiannon Holmes explore the link between proteins and resistance to ocean acidification

Rhiannon Holmes holds up two female Dungeness crabs. Photo by Luke Hollister.

Professor Brooke Love was already studying the effects of ocean acidification on sea life, but wanted to look into some new tools to aid her studies. After Love received the National Science Foundation’s Mid-Career Advancement Grant in 2020, she decided to learn molecular tools such as mass spectrometry to explore a microscopic angle. 

Soon after, she found a study by Paul McElhany, who was researching Dungeness crabs at the National Oceanic and Atmospheric Administration (NOAA). 

McElhany had found a difference in survivability between the offspring, or zoea, of multiple Dungeness crab mothers collected in different regions when living in water with a high concentration of CO₂.  

Close-ups of some zoea used in the experiment. Photos courtesy of Rhiannon Holmes.

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The NOAA group initially hypothesized that water conditions, such as oxygen and CO₂ levels, at the sites where the crab mothers were collected could influence the zoeae’s survivability and resistance to ocean acidification (OA), but ultimately they found that location had less of an impact than matrilineal lineage.  

As Love continued the research, she knew she would need more resources.  Support from the Washington Ocean Acidification Center allowed her to move ahead and bring WWU undergraduate Rhiannon Holmes onto the project as an intern. Together, they took the first NOAA experiment’s preserved zoea gathered from the Puget Sound and compared all the proteins present in each brood. Of the three Puget Sound females, one mother’s brood had far higher survivability under high CO₂ conditions than the other two. The team discovered that these survivors had elevated amounts of a few key proteins.   The function of these proteins could indicate the reason why those zoea survived the best.  

Now, the team is working towards the next phase of their experiment, which will consist of testing the resistance to OA of additional broods to see if the first experiment’s data is repeatable. Love’s team is working with local tribal fishery experts to collect new egg-bearing females and will use the Shannon Point OA system to test how their offspring survive, and to see if their targeted proteins are once again associated with more resilient broods in the next trial.  

“We’ve been using mass spectrometry to look at the different proteins that they produced, and then compare the zoea that were resistant with the vulnerable ones. We identified a group of 33 proteins that were different between the two groups,” said Holmes, who is now a graduate student in Love’s lab. “We’ve only analyzed zoea from one of the three locations so far. They had three females per location, so the sample size is pretty small, but we’re interested in seeing if  that trend holds true as we analyze the rest of the samples.”  

Sampling on the acidified reef. In contrast to the structurally complex control reefs, the seafloor here is relatively flat and dominated by turf algae — habitat that supports far fewer fish and much smaller shoals. Photo by Manabu Ooue and provided by the authorship team.

This blog post is provided by Angus Mitchell and colleagues and tells the #StoryBehindThePaper for the article, “Ocean acidification, more than warming or heatwaves, constrains shoaling behaviour in a range-extending fish through habitat simplification”, which was recently published in the Journal of Animal Ecology. In their study, Mitchell and colleagues reveal the hidden impact that climate change can have on the social lives and shoaling behaviour of reef fish.

Watch a reef long enough and you realise that fish are almost never alone. They move in groups, feed in groups, and react to danger as a group. For small reef fish, being part of a shoal is a survival strategy. More eyes spot predators sooner. More bodies mean any one fish is less likely to be the unlucky one. And fish in bigger groups tend to be bolder, as they forage more efficiently, stay out in the open more, and spend less time hiding.

When we started looking at how climate change affects fish behaviour on reefs experiencing ocean acidification and warming in Japan, we assumed we would find the usual story. Warmer water and rising acidity would alter fish behaviour, make them more cautious, or accelerate their activity levels. That seemed like the obvious prediction.

It turned out to be different — or at least, for schooling species.

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Warming and acidification had little direct effect on behaviour

Across all reef types, even during the heatwave, the fish behaved in much the same way. They kept feeding. They did not suddenly become more nervous. The direct effects of warming, acidification, and heatwave stress on individual behaviour were mostly minimal.

You could read that as good news. Fish holding their own against climate change. But when we looked at what actually caused how the fish were behaving, the answer was not temperature or water chemistry at all. It was how many fish were in the shoal.

Fish in bigger shoals foraged more and hid less. Fish in smaller shoals were more cautious, regardless of the reef conditions around them. Shoal size, not climate stress, was mediating the behaviours we observed.

That sent us back to ask a different question: why were shoals so much smaller on the acidified reef?

What acidification actually does to a reef

On non-acidified reefs, the benthos is structurally complex, a mix of algae, encrusting organisms, and vertical relief that gives reef fish the three-dimensional habitat they rely on. On our acidified reef, that structure was largely gone. The seafloor was dominated by short turf algae, flat and featureless.

There were far fewer fish. Not because the fish were sick or behaving strangely, but because the habitat could not support the same densities we observed on non-acidified reefs. With fewer fish around, the shoals that did form were much smaller: up to 79% smaller than shoals on nearby control reefs. And with smaller shoals came more cautious behaviour across the board.

Oyster farming lines at Lambert Shellfish on the Eastern Shore in Virginia on May 28, 2026. Katherine Hafner/WHRO News

Shellfish farmers are working with the Virginia Institute of Marine Science to better understand the looming issue.

Shellfish such as clams, crabs and oysters need tiny building blocks called calcium carbonate ions to grow and thrive.

These particles are essential to build sturdy shells that protect marine creatures from predators – and make them more appealing for human diners.

But rising acidity tied to climate change is making it harder for shellfish to access those fundamental building blocks.

The issue caught officials’ attention in the late 2000s when acidic corrosion caused mass die-offs of baby oysters in the Pacific Northwest.

Researchers at William & Mary’s Batten School and Virginia Institute of Marine Science have teamed up with local shellfish farmers to learn more about how changing conditions could impact the aquaculture industry in coastal Virginia.

“We know the threat exists,” said Emily Rivest, an associate professor in ecosystem health at the Batten School and VIMS. “This gives us the opportunity to try to get ahead of it to understand how to build our resilience and prevent those kinds of dramatic negative impacts.”

The project is funded by a $1.2 million grant from the National Oceanic and Atmospheric Administration’s Ocean Acidification Program.

The ocean absorbs about a third of the climate-warming carbon dioxide humans release into the atmosphere. That causes a cascade of chemical changes underwater, including reducing pH levels.

For millions of years, the ocean’s pH remained relatively stable at 8.2 on the pH scale, which ranges to 14, the most basic. Since the start of the Industrial Revolution, it has dropped to 8.1. Because the scale is logarithmic, that represents a nearly 30% increase in acidity, according to NOAA.

In much of the Chesapeake Bay, the rate of change is happening even more quickly, particularly in the middle, VIMS previously found.

One factor is freshwater. When freshwater surges into the bay, it lowers the amount of salt in the water, which makes it more susceptible to acidity, Rivest said. That has sometimes affected restored oyster reefs on the western side of the Eastern Shore.

Pollution from nutrients washing off land into the bay compounds the issue by triggering algae that produce carbon dioxide when eaten by bacteria, Rivest said.

Luckily, natural variability in the Chesapeake Bay “has shaped the eastern oyster to be a very tough and resilient species,” Rivest said.

Lab tests indicate local oysters are “much more tolerant of acidification” than out West. The question is: What is their breaking point?

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We are excited to spread the word that BMSC and our partner and neighbor, Nova Harvest, along with the Hakai Institute and the BC Shellfish Growers Association, have received one of the CRBS (Climate Ready BC Seafood) Program Grants! This grant provided funds for research that helps understand the impacts of ocean acidification and hypoxia on the province’s seafood so that we can mitigate the issues and improve the resiliency of organisms that we rely on for food.

The partners are using various ocean observing instruments,  such as the Burke-o-later, to monitor ocean parameters in sea water. This monitoring allows for both research on how shellfish respond to changes and as a daily monitoring tool. Having this live data allows the team to react in real-time, improving the survival of and production of shellfish. 

Watch the video to learn more about the project

Ocean acidification and hypoxia threaten British Columbia’s coastal food security. This short documentary highlights some of the 11 projects funded by a $2M funding envelope provided by the Province of British Columbia to create the Climate Ready BC Seafood Program. Learn more about how these groups are working to further our understand the impacts of ocean acidification and hypoxia in BC to provide knowledge for mitigation and adaptation that supports enhancing the resiliency of BC’s seafood.

Why do we study ocean biogeochemistry?

The ocean has a huge and diverse range of ecosystems, from shallow coastal waters to the vast open sea and the deep seafloor. Each one supports life that’s adapted to its own specific environment and food webs. Ultimately, at the base of almost all marine ecosystems are tiny, microscopic organisms: the phytoplankton.

Why Does the Ocean’s Carbon Cycle Matter?

The ocean plays a dominant role in the Earth’s carbon cycle. It holds more than 90% of the planet’s carbon and absorbs around 25% of our carbon dioxide (CO₂) emissions. This uptake reduces the amount of CO₂ left in the atmosphere to cause climate warming. Understanding how the ocean’s carbon cycle works is a critically important area of research.

Marine ecosystems play a significant part in the ocean’s natural carbon cycle by transporting carbon from the surface to the deep ocean. This process is known as the “biological carbon pump” (BCP). However, climate-driven changes in ocean temperature, circulation, and mixing are expected to reduce the supply of deep nutrients that fuel the BCP. This may disrupt its vital role in storing carbon.”

How Does Ocean Biogeochemistry Affect Human Communities?

Focusing more directly on human concerns, marine productivity is ultimately what provides us with resources like fisheries. Marine ecosystems support global fisheries, which collectively employ 62 million people and feed about 3.2 billion, sustaining regional economies.

In coastal areas, seaweeds provide ecosystem services like pollution remediation and have a natural value we can all appreciate. On top of that, the wider ocean carbon cycle could potentially be leveraged by marine carbon dioxide removal (mCDR) technologies. These aim to remove CO₂ from the atmosphere and eventually help reduce the extent of climate warming.

So, studying how marine ecosystems operate, and how they might change, is a major goal for our ecosystems modelling group.

What is MEDUSA?

MEDUSA (Model of Ecosystem Dynamics, nutrient Utilisation, Sequestration and Acidification) describes the surface ocean ecosystem with a simple, size-based model (nutrient-phytoplankton-zooplankton-detritus). It simulates the linked biogeochemical cycles of carbon, nitrogen, silicon, iron, and oxygen. We use MEDUSA in detailed, high-resolution simulations to help understand how human systems, including fisheries, may change in the future.

MEDUSA is typically run inside physical models of the ocean. This means its components respond to properties like temperature and salinity, and are transported around the ocean by currents. We can then compare the geographical and seasonal output from our models with observational data from ships, autonomous platforms, or satellites. This helps us work out how good a job the model is doing and how we can improve it.

Visit the MEDUSA website

How Does MEDUSA Contribute to Climate Research?

An important part of our work comes from MEDUSA serving as the marine biogeochemistry component of the UK’s state-of-the-art Earth system model, UKESM. Through UKESM, MEDUSA contributes to the international climate simulations that inform the Intergovernmental Panel on Climate Change (IPCC) Assessment Reports. This helps improve our global understanding of how the ocean influences climate.

Using UKESM also allows our group to better study the links between marine ecosystems and the wider atmosphere and land systems. This integrated approach lets us examine how changes in one part of the Earth system cascade through to affect others.

Why is the Research Important for the Future?

Ocean biogeochemistry is important for understanding the ocean’s carbon cycle and its ecosystems, so crucial for both tackling global-scale challenges such as climate change and knowing how we can mitigate these or adapt to them.

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An innovative new research project led by William & Mary’s Batten School & VIMS is bringing together scientists, shellfish farmers and community planners to prepare for emerging environmental challenges related to ocean and coastal acidification (OCA) in the Chesapeake Bay.

“It isn’t something that we’re thinking about on a daily basis, but that doesn’t mean that we shouldn’t begin planning for it now,” said Marcia Berman, co-founder of Cappahosic Oyster Company. “Aquaculture is a vulnerable industry, and more science is always welcome in helping us prepare.”

Supported by a $1.2 million grant from the National Oceanic and Atmospheric Administration’s Ocean Acidification Program, the Regional Vulnerability Assessment (NOAA RVA) study combines traditional coastal and marine science with community research to develop adaptation resources and strategies for the aquaculture industry.

With an advisory committee comprised of Batten School & VIMS experts, members of the region’s shellfish industry and community planners, work is now underway to develop a dynamic, web-based dashboard featuring user-friendly tools that will support businesses and municipalities through complex decision-making processes in the decades ahead.

An invisible shellfish stressor approaches from both land and sea  

OCA is the result of both global and local processes. On a global scale, acidification occurs when the ocean absorbs excess carbon dioxide from the atmosphere, reducing the water’s pH and making it more acidic. In coastal regions like the Chesapeake Bay, freshwater runoff introduces nutrients to coastal waters, inducing processes that can lead to further acidification.

“It’s this hidden stressor sneaking up on us and on the shellfish,” said Rivest, an associate professor at the Batten School of Coastal & Marine Sciences & VIMS and the project’s primary investigator (PI). “Animals like oysters and clams that build their shells out of calcium carbonate provide valuable environmental services and are particularly vulnerable to acidification. Understanding the impact of [OCA] on shellfish, and on shellfish farmers, is critical if we want to support the ecosystems and communities that depend on them.”

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Figure: Paracentrotus lividus with its faecal pellets used to investigate diet with eukaryotic DNA metabarcoding.

Ocean acidification not only affects the physiology of marine organisms but also profoundly transforms their feeding relationships and may intensify competition between species that previously occupied distinct trophic niches. This is one of the main conclusions of the TROIA project (TROphic Interactions of two echinoderms under ocean Acidification), led by Dr. Vanessa Arranz and Dr. Sara González-Delgado from the Marine Biodiversity and Evolution (MBE) group at the Biodiversity Research Institute (IRBio) of the University of Barcelona, and funded through a PR IRBio 2024 Grant.

The study was carried out in the natural CO₂ vent system of Punta de Fuencaliente, on La Palma (Canary Islands), one of the few naturally acidified environments in the Atlantic. In this area, submarine volcanic emissions generate a pH gradient along the coast that allows researchers to simulate the oceanic conditions projected for the coming decades and to study their long-term effects on real marine communities.

The results, currently under publication, show that under acidification the isotopic niche space of the benthic community is significantly reduced. Basal carbon sources become homogenized and functional trophic diversity decreases. “Acidification simplifies the benthic food web: there is less resource variety and organisms converge towards more similar feeding strategies,” explains Dr. Sara González-Delgado.

Two species, two contrasting responses

The study focuses on two sea urchin species common in the Mediterranean and the Atlantic: Paracentrotus lividus and Arbacia lixula. The results reveal contrasting responses to acidification. While P. lividus maintains a relatively stable diet along the pH gradient, A. lixula undergoes a notable dietary shift, moving from a predominantly carnivorous diet under current conditions (around 79% animal prey) to herbivory in acidified environments. This shift leads to an increase in trophic niche overlap between the two species, rising from 0% under current conditions to more than 27% in the most acidified sites. “Arbacia lixula is highly trophically plastic, but this flexibility comes at a cost: under acidification it begins to compete for the same resources as Paracentrotus lividus,” notes Dr. Vanessa Arranz.

Combining methods to better understand diet

The project combined two complementary methodological approaches: stable isotope analysis (δ¹³C and δ¹⁵N) and eukaryotic DNA metabarcoding from fecal samples. One of the study’s key contributions is the first validation in these species of using feces as a non-invasive sample to study diet through COI gene metabarcoding.

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Ecological implications in a changing ocean

The results have important implications for predicting changes in marine communities under the acidification scenarios projected by the IPCC. The study highlights the need to go beyond individual physiological effects and also consider how trophic interactions and the ecological roles of species are altered within marine ecosystems.

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Winter School lecturer Sam Dupont, from the University of Gothenburg, demonstrates a technique for an experiment on sea urchin fertilization. (Photo: IAEA)

The IAEA is training early-career scientists to assess the impacts of ocean acidification and pollution, helping countries respond to environmental changes.

Marine biodiversity faces growing pressure from environmental changes and pollution. To help countries understand and respond to these combined threats, the IAEA is equipping young scientists with advanced skills to study the ocean’s most pressing challenges.

The Ocean Acidification International Coordination Centre (OA-ICC) trained 14 early-career scientists from around the world in key concepts and cutting-edge techniques to assess the impacts of environmental changes from multiple stressors on the ocean. The third edition of the OA-ICC Winter School on Ocean Acidification and Multiple Stressors was held at the IAEA Marine Environment Laboratories in Monaco from 24 November to 5 December 2025. 

Threats to Ocean Health

The ocean faces multiple pressures, including from acidification, warming and pollution. These stressors threaten biodiversity and food security in many regions. Understanding their combined effects is essential to develop effective mitigation and adaptation strategies. 

“Ocean acidification is not occurring in isolation, but expertise in studying multiple stressors is often lacking. The OA-ICC capacity building programme plays a key role in expanding this knowledge base,” said Lina Hansson, Associate Project Officer at the IAEA.

During the two-week course, participants learned best practices in experimental design and applied them in a hands-on laboratory study. They investigated the combined effects of ocean acidification, warming and lithium pollution on the reproductive success of a common Mediterranean Sea urchin. 

Participants also visited the Laboratoire d’Oceanographie de Villefranche (LOV) in France for practical training in seawater chemistry monitoring and connected with researchers at the Centre Scientifique de Monaco. The Winter School emphasized science communication and community engagement. Through a series of guest lectures, participants explored principles for co-designing research, including integrating traditional knowledge from local communities.

“The Mediterranean Sea is heavily affected by multiple stressors. Record-breaking marine heatwaves, pollution, combined with acidification, have led to mass mortality of key species,” said Steeve Comeau, Research Scientist at LOV and Winter School lecturer. “Training this new generation in multifaceted experimental approaches is critical for predicting future impacts.”