The Hidden Architects of the Ocean Carbon Cycle
Uria Alcolombri
The Hebrew University of Jerusalem, Israel
Winning article: Microbial dietary preference and interactions affect the export of lipids to the deep ocean (Science, 2024)
“The urgency of climate change demands that we explore every possible avenue for carbon sequestration. Marine bacteria, though microscopic, play an outsized role in this process.”
Deep in the ocean, an invisible process regulates Earth’s carbon storage, yet it remains one of the greatest uncertainties in climate science. When we think about climate change, we often focus on forests, fossil fuels, and rising temperatures. However, hidden beneath the ocean’s surface, a microscopic world plays a crucial role in regulating Earth’s climate, despite being largely invisible to us. Phytoplankton drive nearly half of the planet’s photosynthesis, capturing atmospheric CO₂ and forming the foundation of the oceanic food web. Through several processes collectively known as the biological carbon pump, a portion of this carbon aggregates into sinking particles that transport it to the deep ocean, where it can be stored for thousands of years. At its core, the gravitational part of this pump serves as a natural carbon sequestration system, but many aspects of how carbon travels from the surface to the deep sea remain poorly understood.
One of the key missing links is the role of marine bacteria in breaking down sinking particles and the organic matter they contain, particularly lipids, which are abundant components of sinking carbon. Scientists have long assumed that this process occurs uniformly, with all organic material degrading at the same rate. However, our research, published in Science, challenges this assumption. We discovered that bacteria have distinct dietary preferences and complex interactions, which significantly influence how much carbon ultimately reaches the deep ocean and how much is released back into the atmosphere. This study was a truly collaborative effort, bringing together an international team of experts in microbiology, biophysics, oceanography, biochemistry, and mathematical modeling to address a fundamental question in Earth system science.
Bacteria have a taste for lipids. Lipids are among the most energy-rich molecules in the ocean, serving as fuel reserves and structural components of cells. However, until now, the role of bacteria in lipid degradation has remained an overlooked aspect of the biological pump. By combining nano-lipidomics, an advanced technique for tracking changes in lipid composition, with cutting-edge microscopy, we found that not all bacteria degrade lipids in the same way. Some are highly selective, targeting specific lipid types, while others are generalists, breaking down a wide range. Even more surprisingly, bacterial interactions can either speed up or slow down lipid degradation, ultimately affecting how much carbon is locked away in the deep sea.
To test this, we built synthetic microbial communities in controlled lab setups, combining different bacterial species with phytoplankton-derived lipid droplets. The results were striking. Some bacteria worked together, breaking down lipids more efficiently than they could alone. Others interfered with one another, slowing the process. When we incorporated these findings into a mathematical ocean carbon transport model, we saw how much microbial metabolism influences global carbon sequestration. If certain bacteria degrade lipids too quickly, more carbon is released back into the water column, reducing the amount reaching the deep ocean. But if microbial interactions slow down degradation, more carbon is retained at depth. This means that the composition of bacterial communities is not just a niche scientific curiosity; it is a fundamental factor shaping the planet’s carbon cycle.
Figure 1: A close-up view of a lipid droplet (red) surrounded by tiny marine bacteria (yellow) that feed on it and interact with one another for their survival. Each bacterium measures just about 2 micrometers in length, highlighting the microscopic scale of these interactions. The lipid, extracted from the diatom species Phaeodactylum tricornutum, serves as a carbon source, fueling the metabolism of these tiny bacteria as they break it down for energy. Image Credit: Dr. Uria Alcolombri, Dr. Lars Behrendt, Dr. Steven Smriga, and Prof. Roman Stocker.
Our findings contribute to the endeavor to keep Earth’s systems within the safe operating space of our planetary boundaries. Climate change is a critical concern among these boundaries, and the ocean’s capacity to store carbon plays a key role in regulating it. Current models do not fully account for how microbial metabolism affects carbon sequestration. They often assume organic matter degradation is uniform, overlooking the reality that different bacteria break down lipids at different rates through complex interactions. If models fail to capture these nuances, they could overestimate or underestimate the ocean’s ability to store carbon, leading to inaccurate projections of future CO₂ levels. By improving our understanding of microbial lipids and other organic matter degradation and anticipating changes in ocean microbiomes over the coming century, we can refine ocean carbon pump models and develop better strategies for protecting and enhancing the ocean’s role as a carbon sink.
Where do we go from here? Understanding microbial carbon cycling has real-world implications for climate solutions. Refining climate models by integrating microbial metabolism into Earth system models will lead to more accurate predictions of how the biological carbon pump responds to climate change, helping to shape effective climate policies and carbon offset strategies. While large-scale ocean-based carbon sequestration technologies are still in development, our research highlights natural processes that help lock carbon away in the deep ocean. If scientists can one day safely harness these mechanisms, we may be able to optimize carbon storage, potentially through the promotion of phytoplankton blooms or engineered microbial communities that enhance carbon export. Our findings also underscore the importance of protecting marine microbial ecosystems that act as natural carbon sequestration hotspots, ensuring the ocean continues to function as a vital carbon sink. By fostering collaboration between scientists, policymakers, and industry leaders, we can leverage microbial science for climate resilience, turning microscopic interactions into powerful tools for planetary health.
Small microbes have a big impact. Microbes are often overlooked in climate discussions. We focus on reforestation, renewable energy, and emissions reductions, all vital efforts. But the ocean, covering 70% of Earth’s surface, is a vast reservoir for carbon storage, and its efficiency depends on the unseen world of marine microbes. What we have learned so far is just the beginning. If we want to truly understand how the ocean will respond to climate change, we need to study life at the microscopic scale, the scale where bacteria rule. These tiny organisms shape carbon fate in the ocean, and in doing so, they shape the future of our climate. By continuing to unravel the complexities of microbial interactions, we can work toward a sustainable, informed approach to climate mitigation, one that embraces the power of nature’s smallest architects.
The urgency of climate change demands that we explore every possible avenue for carbon sequestration. Marine bacteria, though microscopic, play an outsized role in this process. By better understanding their interactions and metabolism, we can refine climate models, protect crucial ocean ecosystems, and explore nature-based solutions for carbon storage. This is why microbial oceanography isn’t just about studying the unseen; it is about uncovering the fundamental processes that shape our planet’s future. If we get this right, it could change the way we approach climate action, showing that even Earth’s smallest life forms have a massive impact on global climate stability.
Figure 2: Single Particle Degradation Experiment – North Atlantic. Conducted during the AR16 Cruise in May 2017 aboard the R/V NEIL ARMSTRONG, operated by the Woods Hole Oceanographic Institution (WHOI), MA. The experiment was led by Dr. Lars Behrendt, Dr. Jonathan E. Hunter, and Chief Scientist Prof. Benjamin A. S. Van Mooy. Photo credit: Lars Behrendt and Jonathan E. Hunter.