How Decaying Shells Help Preserve the Alkalinity of the Seas

Calcium carbonates produced by sea creatures help to maintain the ocean's alkalinity — and also serve as a natural sink for anthropogenic carbon dioxide. To better understand essential but obscure deep-sea biogeochemical processes, Olivier Sulpis of Utrecht University developed an innovative 3D reactive-transport model that shows how seashells help preserve calcite grains in seafloor sediments.

by Alan Petrillo
November 2022

Where is the boundary between an organism and its environment? Usually, our eyes seem to be able to answer this question for us. We can visually distinguish trees from the soil, birds from the sky, and seashells from the sea, but appearances can deceive. We may see hard borders between living and nonliving things, but look deeper: The seemingly solid edges of organisms are actually a porous weave that is as beautiful and profound as any tapestry can be.

Organisms become what they are by exchanging matter with their environments, and this cycle reshapes those environments as well. Our eyes and minds may struggle to perceive what is going on at a molecular level, but the impact of life’s interplay with the environment can be enormous — perhaps as big as the ocean itself.

The Small but Significant Sea Butterfly

Consider, for example, the sea butterfly. “It is like a miniature snail we would see on land, but with wings to fly around in the water,” says Olivier Sulpis, a geochemistry researcher in the Department of Earth Sciences at the Netherlands' Utrecht University. Sea butterflies (also called pteropods) are less than 1 cm long, and they produce their thin, translucent shells from aragonite, which is a form of calcium carbonate (CaCO3).

Figure 1. An example of a sea butterfly. Its wing-like protrusions, which propel it through the water, are called parapodia. Note that the pteropod's aragonite shell is nearly transparent. Image by Russ Hopcroft, University of Alaska, Fairbanks, in the public domain via Wikimedia Commons.

Sea butterflies synthesize aragonite from materials found in seawater, including calcium and carbon. When pteropods die, the dissolution of their aragonite shells neutralizes some of the CO2 (which is an acid) that is suspended in seawater. In this way, the world's vast population of sea butterflies helps to maintain the alkalinity of the ocean. But rising oceanic CO2 levels could upset the conditions that enable sea butterflies to produce their shells in the first place. A shrinking population of aragonite producers could thereby add to a vicious cycle of accelerating acidification.

“We say of sea butterflies that they are ‘first responders’ of ocean acidification because they are so vulnerable,” says Sulpis. Unfortunately, humanity is struggling to interpret what these first responders may be telling us. Sea butterflies are abundant, but much about them remains a mystery, especially after they die and sink to the deepest parts of the ocean. One theory proposes that dissolving aragonite shells trap and neutralize CO2 by interacting with calcite (another form of CaCO3) found in seafloor sediment.

This galvanic deep-sea process could be even more important to maintaining oceanic alkalinity than the reactions that occur while the creatures are alive. Micrometer-scale chemical processes are very difficult to study, especially when they take place 1 km or more underwater. To better understand this elusive phenomenon, Sulpis has developed a novel 3D model (presented in a March 2022 article in Nature Communications) of how aragonite interacts with calcite-rich sediments on the seafloor. (Ref. 1)

Even in Death, CaCO3 Producers Help Sustain Ocean Life

Sea butterflies may seem like an unlikely subject for such intense study, but they and their fellow CaCO3 producers have an outsized impact on their environment. During their lives, pteropods cycle through a vertical commute, rising toward the surface at night and descending during the day. They feed on microorganisms and draw calcium and dissolved carbon from the ocean to build their fragile aragonite shells. (See Figure 2.)

Figure 2. An illustration of pteropods' role in the oceanic carbonate cycle. Living sea butterflies draw calcium and carbon dioxide from sea water to build their shells, which consist of calcium carbonate in the form of aragonite. After pteropods die, their shells sink to the seafloor, where their CaCO3 shells decompose. This decomposition helps sustain the alkalinity of the oceans and builds up carbonate-rich sediments over time.

"In seawater, calcium and dissolved carbon are everywhere," says Sulpis. "This makes them ideal ingredients for organisms to use in building crystal structures." Calcium carbonate compounds make up many seashells, as well as the exoskeletons formed by corals.

The world’s coral reefs are perhaps the most visible oceanic examples of an interwoven tapestry of living and inanimate matter. A healthy reef features living corals that actively synthesize crystal structures from calcium and dissolved carbon. A healthy reef also contains dead corals, which continue to interact with their surroundings as they decay. Along with sustaining a diverse ecosystem of plant and animal life, decomposing corals help maintain the ocean's alkalinity and add to the carbonate-rich sediments that cover the seafloor. Dead pteropod shells also contribute to these sediments, though their exact role is actually rather mysterious.

Figure 3. A healthy coral reef has living corals as well as calcium carbonate structures left behind by now-dead corals. Image by Kristin Hoel via Unsplash.

The Case of the Missing Aragonite

Most corals produce their skeletons from calcite, which is the most common CaCO3 compound found in the oceans. As noted earlier, sea butterfly shells are made from aragonite. “Aragonite and calcite are both CaCO3 compounds, but their crystal structures are different. It is as if they are made from the same bricks, but those bricks are not arranged the same way,” Sulpis explains. From his perspective, aragonite deserves more consideration for its role in the oceanic carbonate cycle.

“We do not know a lot about aragonite, but we are able to estimate how prevalent it is in the shallower waters, where the sea butterflies live,” Sulpis says. “We can also confirm that their shells sink and reach the deep ocean. When we recover sample cores from deep ocean sediments, there is plenty of calcite, but the aragonite we would expect to find is not there. So where does it go?”

Figure 4. A schematic of the molecular structure of calcite. Image by Materialscientist, licensed under CC BY-SA 3.0 via Wikimedia Commons.

One possible explanation for the “missing” aragonite is that the more soluble aragonite shells dissolve faster than calcite at the seafloor, releasing alkalinity and raising the CaCO3 saturation of the seawater in the process, thereby protecting calcite from dissolving. If ocean acidification slowed down aragonite shell production and thereby also the "galvanizing" effect of aragonite dissolution, then calcite dissolution would have to make up for more of the CO2 neutralization at the seafloor than it actually does. But while this theory seems plausible, the challenges of studying the oceanic aragonite cycle make it difficult to prove.

An "Embarrassing" Gap in Knowledge About Aragonite Cycling

In a March 2022 Twitter post (Ref. 2) about his work, Sulpis wrote, “It is embarrassing how little is known about open-ocean aragonite cycling.” When asked about this comment, he laughs and explains, “If you look at published literature, you will find estimates that say aragonite makes up 10% of all the calcium carbonate in the ocean. But you will also find studies that say it makes up 90% of all calcium carbonate! When that is the range of the best expert estimates, yes, it is quite embarrassing!”

Humanity’s spotty knowledge of aragonite cycling is rooted in the difficulty of conducting research in the deeper parts of the ocean. We have limited ability to place sensitive instrumentation in locations so far below the surface. Sulpis says, "Observing reactions in seawater at this scale and depth is nearly impossible, as they occur in an environment where we can’t physically go.” Physically removing specimens from deep-sea sediment is also challenging, especially when the materials to be studied are so fragile. “It is really hard to recover sea butterfly shells with a sediment trap,” says Sulpis. “By the time you bring them up from the deep, they will likely already have dissolved. So, there is a lack of good data about calcium carbonate reactions at deep sea pressures and temperatures.”

While there have been previous attempts to mathematically model the behavior of calcium carbonate in seawater, existing models are of somewhat limited value for Sulpis's research. "Most models have treated all CaCO3 as calcite, rather than creating separate models of aragonite. Also, existing diagenetic 'continuum' models do not capture what is happening at the scale of a single grain, or a single pore in a seashell," he explains.

Another issue is that older models have rendered CaCO3 grains as smooth, uniform objects, which is not accurate. “We know that these grains are definitely not smooth cubes or spheres. They are complex and heterogenous micrometer-scale shapes with insides and outsides." Sulpis does acknowledge that some simplifications are necessary, but says, "We wanted to replicate the actual shapes as closely as possible, at the smallest scale possible. Before deciding to simplify some structures, we wanted our simulation to confirm that these simplifications would not compromise results.”

A Simulated Deep Dive into the Ocean-Sediment Boundary Zone

For a deeper understanding of how calcite and aragonite interact at the seafloor, Sulpis developed a 3D model using the COMSOL Multiphysics® software. This model makes it possible to move virtually among the boundaries between oceanic organisms and their environment. It enables researchers to simulate the dissolution reactions occurring among aragonite and calcite grains and the seawater that surrounds them. The water's alkalinity, density, and chemical composition were set to match typical deep-sea conditions. The team modeled various solids and simulated their interactions with seawater and seafloor sediment. Sulpis also added seashell models, based on scans of actual specimens, to his sediment–water interface. The H. inflatus pteropod shell highlighted in Figure 5 below, for example, is based on a CT scan of a specimen from the Cariaco Basin off the coast of Venezuela. Such 3D images enabled the simulation to capture how the irregular shape of a shell could affect its dissolution.

Figure 5. Simulation images of four pteropod species' seashells, showing changes after being submerged for one minute. The highlighted H. Inflatus shell is made from aragonite, while the others are calcite. The top row of images shows CaCO3 saturation levels (in blue) in the surrounding seawater, and the bottom row shows the rate at which the shells dissolve. Note that the intricate inner shapes of the shells appear to have little effect on saturation levels.

The simulation indicates that the inner shape of a shell may not have a significant impact on how it reacts with seawater. “If you look at the top row, it tells us that inside these shells, the trapped water can become completely saturated with CaCO3. This prevents further dissolution from occurring along the complex inner surface, and so the shells dissolve from the outside in,” Sulpis says. These results suggest that some simplification of a shell’s modeled shape will not necessarily affect simulation results, at least when the shell is completely surrounded by seawater.

Now, what happens when a mix of seashells and seawater is added to calcite-rich sediment? Figure 6 presents the simulated effects of this interaction. In image (b), a dissolving sea butterfly shell is shown to exert a galvanizing action on calcite grains mixed into the sediment. These grains were rendered as spheres — a simplification that Sulpis made based on the results of simulations such as those in Figure 5.

Figure 6. Image (a) shows the tendency for calcite dissolution above, at, and below the sediment–water interface. The black plot line shows that, in the absence of aragonite, calcite will continue to dissolve. The red line shows how the presence of the shell shown in image (b) will prevent calcite from dissolving. Image (b) is from a simulation showing how a dissolving pteropod shell affects the boundary zone around the sediment–water interface. The circles represent grains of calcite suspended in the sediment. Areas shaded red indicate where the dissolution of calcite grains is being prevented by the presence of aragonite.

The seawater that mingles with solids near the sediment–water interface plays a crucial role in this process. “Existing 1D models make the boundary between seafloor and the water look like a perfect solid line,” he says. In reality, the boundary is varied and seawater is circulating around solids, even below the apparent line of separation. Capturing the gradated boundary between seawater and sediment is one of the advantages of Sulpis’s 3D model. As the pteropod shell dissolves, the surrounding seawater becomes saturated with aragonite. This zone of saturated seawater mixed with sediment is indicated by the red shading in Figure 6 (b). It is this aragonite-saturated seawater that chemically interacts with — and protects — the calcite left behind by other organisms.

Image (a) in Figure 6 shows the seawater saturation state with respect to calcite, which is its ability to be dissolved throughout this transition zone between sea and sediment. At 1.5 mm above the seafloor, seawater is undersaturated, and any calcite grains should dissolve quite readily. The black line shows that in the absence of any aragonite source, calcite dissolution should continue at the sediment–water interface. The red line indicates the zone where pteropod shell dissolution should arrest the dissolution of suspended calcite grains, because of the supersaturation it generates.

Figure 7. Simulation results showing how the presence of a pteropod in the seafloor sediment affects the dissolution rates of nearby calcite grains. Lighter-colored areas indicate where dissolution is occurring more rapidly. The white lines indicate the saturation line, or isocontour, where calcite is at equilibrium with its dissolution byproducts, meaning there should not be any net dissolution or precipitation.

Helping Other Humans Mend the Seas

Having developed a new means of analyzing underwater micrometer-scale biochemical processes, Sulpis is now exploring how his work can guide further research. “Our next step has been to try to replicate these processes in the lab, with calcite and pteropod shells in beakers. So far, experimental results are similar to what the simulation shows,” he says. “The goal now is to use this information to better interpret what we can observe in situ.” Toward this end, Sulpis and his colleagues have obtained a grant from the Dutch Research Council (NWO) to directly study how aragonite producers shape their environment.

Of course, the organism whose activity has the greatest impact on its environment is the human. Anthropogenic acidification threatens the life-sustaining tapestry that ocean creatures weave among their parts of the Earth. With this in mind, the broader project of understanding carbonate cycles takes on added urgency. “Compared to how much CO2 we are adding to the oceans, only a tiny amount is being neutralized," says Sulpis. "Maybe the carbonate cycle process could do the job, but it may take several thousand years to do so!”

Taking a more immediate perspective, Sulpis is eager for fellow humans to apply his research and analysis to protecting the sea butterflies' world — and ours. “Our models are all open access,” he says, “and I hope others can make use of what we have created."

Olivier Sulpis's simulations of calcium carbonate seashell dissolution are available for download at


  1. O. Sulpis et al., “Aragonite Dissolution Protects Calcite at the Seafloor”, Nature Communications, vol. 13, no. 1104, 2022;
  2. O. Sulpis, [@OliverSulpis], (2022, Mar. 7), It is embarrassing how little is known about open-ocean aragonite cycling. Published estimates of the fraction of aragonite in [Tweet], Twitter;