On World Ocean Day, we celebrate the power of marine microbes

In the face of the climate crisis, there is growing interest in understanding how nature manages carbon, and the ocean is one of its most powerful and underappreciated tools. At the VIB-KU Leuven Center for Microbiology, the team of Sammy Pontrelli is working to understand exactly how it does so, at the level of molecules and microbes.

“When people think about the ocean and climate, they often picture currents, ice melt, coral reefs, or rising sea levels. But one of the ocean's most critical climate functions is its capacity to absorb and store enormous amounts of carbon,” explains Sammy.

The ocean isn't passive in this process; it is an active, living system, and microbes are at the controls.

A carbon story that starts with sunlight

The story begins with phytoplankton, microscopic plant-like organisms that capture carbon dioxide from the atmosphere through photosynthesis. “Remarkably, these tiny cells are responsible for roughly half of all photosynthetic carbon capture on Earth, matching the combined output of every forest, grassland, and plant on land.”

Once that carbon enters the ocean, what happens to it is anything but simple: “Some of it gets broken down by microbial cells for energy and released back into the water and air as CO₂, essentially the ocean's version of breathing. Some is released as molecules that feed bacteria at the base of the food web, passing carbon up through the ecosystem. Some becomes the physical bodies of algae and bacteria themselves, which can clump together and sink to the seafloor as particles, locking carbon away in deep sediments for thousands of years.”

But then there is something stranger and in many ways more remarkable, Sammy adds: some of that carbon resists consumption entirely. “It accumulates as an enormous pool of small dissolved molecules floating through the ocean's waters, a reservoir so vast that it contains more carbon than all of the plants on land combined. These molecules can persist for thousands of years, effectively acting as a long-term carbon buffer that helps protect us from the full force of climate change.”

One of the ocean's great mysteries

What makes this reservoir so puzzling, and so fascinating, is that we barely understand its dynamics. “These dissolved molecules have extraordinary and complex chemical structures. We know remarkably little about how microbes actually build them, through what cellular processes and chemical reactions, or why they are so resistant to being broken down by other microbes.”

“Even stranger, despite their apparent stability, these molecules are on average only about 5,000 years old and not nearly as ancient as you might expect for something so persistent. Why? We don't yet know.”

By studying how marine microbes naturally contribute to long-term carbon storage, Sammy Pontrelli and his team hope to uncover the biochemical rules, the molecular knobs and levers, that determine where carbon goes and why.

What controls the fate of carbon?

The lab's research works on two levels. At the biochemical level, they investigate how marine enzymes transform carbon-containing molecules, tweaking their structure in ways that can make them easier or harder for other microbes to consume. At the microbial community level, they examine how interactions between microbes collectively shape which carbon compounds accumulate and which disappear.

“Together, these processes help explain how carbon is shunted between different fates: released as CO₂, cycled through the food web, buried in sediments, or locked away in that vast dissolved reservoir. Understanding these mechanisms is not just scientifically fascinating, but increasingly urgent.”

Microbial behavior at scale

Answering these questions requires the ability to study microbial behavior across many strains, conditions, and timepoints at once.

Microbiology experiments can quickly grow into hundreds or thousands of samples, making detailed molecular characterization a major bottleneck. Using high-throughput liquid chromatography mass spectrometry (LC-MS) platforms, the lab can analyze more than 400 samples per day. Combined with enzyme assays, this allows the team to profile both the internal chemistry of microbial cells and the molecules they release into their environment, across diverse species and conditions at scale.

“This is how we get our hands on the knobs and levers, systematically mapping how changes in enzymes, microbial interactions, and environmental conditions shift the fate of carbon molecules.”

But the insights don't stop at the ocean. By studying these processes at such resolution and scale, the lab aims to extract fundamental principles about how microbes work, how they compete, cooperate, adapt, and reshape their chemical environment.

“The same understanding that helps explain carbon cycling in the ocean may also inform how we think about engineering microbes for other purposes, from industrial biotechnology to other natural environments where microbial chemistry shapes the world around us.”

Thirty years from now

As climate change accelerates and human activity reshapes marine environments, a critical question emerges: how stable is this enormous carbon reservoir, and what could tip it in the wrong direction? Understanding the biochemical mechanisms that control carbon fate in the ocean is the kind of knowledge that feeds directly into the models scientists use to predict how the ocean's carbon storage capacity will respond to rising temperatures, shifting ocean chemistry, and changing ecosystems, giving us a clearer window into what the future may hold.

“There is growing interest in deliberate interventions in the ocean to draw down more atmospheric carbon, things like fertilizing the ocean with iron to stimulate algal growth, or artificially circulating deep nutrient-rich waters to the surface,” Sammy says. “These ideas are not without merit. But they also carry real risks. If we alter the balance of microbial activity in the ocean without understanding the underlying biochemistry, we could inadvertently disrupt the very cycles that make the ocean such an effective carbon store, or worse, trigger the breakdown of carbon that has been safely locked away for millennia.”

By identifying the molecular mechanisms that control carbon fate at the level of individual enzymes and microbial interactions, Sammy and his team aim to build a clearer picture of what drives these processes and what happens when they are disturbed, both to anticipate the consequences of a changing climate and to evaluate the risks and promise of deliberate intervention.

“World Ocean Day is often a moment to reflect on the beauty, biodiversity, and vulnerability of marine ecosystems. But it is also a reminder that the ocean is a living, dynamic engine in the Earth system, and that some of its most important climate functions depend on microscopic life.”

As VIB marks 30 years of science for a better future, this kind of research captures an important part of that mission: fundamental biology with the potential to shape how we think about tomorrow's challenges. In the years and decades ahead, understanding the biochemical rules that govern carbon in the ocean may be one of the most important things we can do to prepare for and navigate a changing climate.

Liesbeth Aerts

Research communicator

• liesbeth@beakon.be