Phage-Resistant Marine Bacteria Can Still Help Sink Carbon to the Ocean Floor
Marine bacteria may be microscopic, but they play an outsized role in regulating Earth’s climate. A new scientific study shows that even when these bacteria evolve resistance to viral infections, they can still actively contribute to one of the ocean’s most important climate processes: transporting carbon from surface waters to the deep sea. In some cases, this resistance may even enhance that process rather than weaken it.
The research, published in Nature Microbiology in 2025, explores how marine bacteria respond to constant attacks from viruses known as bacteriophages, or simply phages, and what those responses mean for the ocean’s ability to store carbon long-term.
Why Marine Bacteria Matter for Carbon Cycling
The ocean absorbs a massive amount of carbon dioxide from the atmosphere. Much of this carbon enters marine food webs and is processed by microorganisms. Marine bacteria are key decision-makers in determining whether that carbon is quickly recycled back into the atmosphere or transported downward into deeper ocean layers, where it can remain locked away for decades or even centuries.
This downward movement of carbon is part of what scientists call the marine biological pump. When carbon-rich particles sink, they remove carbon from surface waters and reduce how much CO₂ eventually returns to the air.
However, marine bacteria operate under constant pressure. Oceans are filled with phages, and these viruses infect bacteria at enormous rates. To survive, bacteria mutate, setting off a continuous evolutionary arms race between viral attack and bacterial defense.
The Big Question Behind the Study
Scientists have long wondered whether phage resistance comes at a cost. If bacteria must alter their structure or metabolism to survive viral infections, does that reduce their ability to perform essential ecological functions, such as carbon capture and sinking?
This new study set out to answer exactly that question by examining how different phage-resistance strategies affect bacterial behavior, especially behaviors linked to carbon export.
The Model System Used in the Research
The researchers focused on a marine bacterium called Cellulophaga baltica, a species commonly used as a model for studying ocean microbial processes. Thirteen phage-resistant mutants were evolved from a wild-type strain of this bacterium after infection with two ecologically relevant phages, known as phi18:1 and phi18:4.
By isolating and studying these mutants, the research team could closely analyze how specific genetic changes influenced bacterial growth, surface properties, metabolism, and sinking behavior.
Two Very Different Ways to Resist Viruses
The study identified two main categories of phage-resistance mutations, each with distinct biological and ecological consequences.
Surface mutations altered structures on the outside of bacterial cells. These structures normally act as entry points for phages. By changing them, bacteria effectively prevent viruses from attaching or injecting their genetic material. These mutations provided broad resistance, meaning the bacteria became resistant to several different phages at once.
Metabolic mutations, on the other hand, occurred inside the cell. In these cases, phages were still able to enter the bacterium, but they could not successfully complete their replication cycle. The virus entered, but it failed to produce new viral particles. These mutations tended to provide narrow resistance, usually protecting against only one specific phage.
The Surprising Discovery About Stickiness and Sinking
One of the most striking findings of the study was that both types of mutations made bacterial cells stickier. Increased stickiness causes bacteria to clump together or attach to particles in seawater. These aggregates are heavier and sink more easily, carrying carbon downward.
However, the effect was much stronger for surface mutants. These bacteria showed a dramatic increase in sinking rates, making them especially effective contributors to carbon export.
This observation is important because previous research has shown that virus abundance is one of the strongest predictors of carbon export in the ocean, even stronger than the abundance of many larger organisms. Until now, scientists did not fully understand why. The new findings suggest that viral pressure may indirectly promote carbon sinking by selecting for bacterial traits that enhance aggregation and sinking.
A Closer Look at Metabolic Resistance
The study also provided rare insight into intracellular phage resistance, an area that has received far less attention than surface-based defenses.
One of the metabolic mutations affected the synthesis of a specific amino acid involved in producing lipids. Lipids are essential components of bacterial membranes and also play a role in viral assembly. When this lipid balance was disrupted, phages were unable to assemble new viral particles inside the host cell.
This suggests that phages depend heavily on host metabolism, and even small disruptions can shut down viral replication entirely. While these metabolic mutants did not sink as rapidly as surface mutants, they still altered bacterial physiology in meaningful ways.
Resistance Comes With a Cost
While phage resistance provided obvious survival benefits, it also came with trade-offs. All resistant mutants grew more slowly than the original, non-mutated bacteria.
The growth penalty was especially pronounced in surface mutants, which, despite their broad resistance and enhanced sinking ability, paid the highest cost in terms of reduced growth rate. Slower growth can ripple through microbial communities, affecting competition, nutrient cycling, and food-web interactions.
This highlights an important ecological balance: bacteria gain protection from viruses, but that protection reshapes how they interact with their environment and with other organisms.
Implications for the Ocean and Climate
The findings add a new layer of complexity to our understanding of the marine carbon cycle. Viruses are often viewed mainly as agents of destruction that kill microbes and release organic matter back into the water. This study shows they also play a constructive and indirect role by influencing which bacterial traits are favored by natural selection.
By promoting bacterial traits that increase sinking, phages may help regulate how efficiently carbon is transferred to the deep ocean. This means viruses are not just passive players but central components of ocean biogeochemistry.
Why This Research Matters Going Forward
Understanding these processes is critical in the context of global climate change. The ocean is one of Earth’s largest carbon sinks, and even small changes in microbial behavior can have large-scale consequences.
The study also opens the door to further exploration of metabolic resistance mechanisms, which remain poorly understood. Expanding research to include more bacterial species and phage types could reveal additional resistance strategies and deepen our understanding of how microbial evolution shapes Earth’s climate system.
Additional Context: The Viral Shunt and Marine Microbial Ecology
This research connects closely to the concept of the viral shunt, a process where viral infections redirect organic matter away from higher trophic levels and back into microbial loops. While the viral shunt often keeps carbon near the surface, this study shows that viral pressure can also enhance pathways that send carbon downward.
Marine microbial ecosystems are incredibly dynamic, and bacteria, phages, predators, and environmental stressors all interact simultaneously. Studies like this highlight why microbial interactions must be included in climate models if we want accurate predictions of future ocean behavior.
Research Paper Reference
Urvoy, M. et al. (2025). Phage resistance mutations in a marine bacterium impact biogeochemically relevant cellular processes. Nature Microbiology. https://doi.org/10.1038/s41564-025-02202-5
