Ocean microbes find ways to survive nutrient scarcity

Ocean research often focuses on large creatures or dramatic events, yet many quiet forces shape the planet in far more powerful ways.

Ammonia-oxidizing archaea belong to this hidden world. These microbes are found throughout the ocean, from crowded coasts to the silent open ocean. Their presence in nutrient-poor regions has confused scientists for years.

In the open ocean, ammonium – the microbes’ known energy source – is often nearly absent, making their survival a long-standing mystery. A new study now offers a clear explanation.

How ocean microbes survive

Researchers at the Max Planck Institute for Marine Microbiology found that some ammonia-oxidizing archaea use urea in addition to ammonium. This simple detail changes the story entirely.

Urea offers another nitrogen source. It also supports energy production when ammonium sinks to extremely low levels.

The team focused on two major groups: Nitrosopumilus in coastal regions and Nitrosopelagicus in open waters. These two groups dominate huge areas of the ocean, yet each behaves in its own way.

To capture these differences, the researchers sampled three contrasting marine environments.

The Gulf of Mexico offered nutrient-rich water and plenty of ammonium. The Angola Gyre showed the opposite extreme, with almost no available ammonium.

The Black Sea provided a layered environment, with ammonium at depth but nearly none near the surface. This variety allowed the researchers to observe how each group performs under different nutrient conditions.

Life in nutrient-poor regions

Nitrosopumilus shows a straightforward pattern. “Nitrosopumilus grows fast when ammonium is available. It is thus well-equipped for life in high-ammonium coastal waters,” said study first author Joerdis Stuehrenberg.

This group fits well into nutrient-rich coastal zones where fresh nutrients arrive often. Nitrosopelagicus follows a more flexible pattern. It takes up ammonium and urea equally well and does not wait for ammonium levels to drop.

Even when ammonium remains abundant, this group continues using urea. This behavior gives it a strong advantage in regions where nutrient levels swing widely or drop to almost nothing.

“Nitrosopelagicus cells have more options,” says co-author Katharina Kitzinger. “If both ammonium and urea are present, they may even double their growth rates by using both at once.”

Nitrification rates in the ocean

This discovery also affects how scientists look at nitrification in the ocean. Most measurements only consider ammonium.

If urea supports far more activity than earlier models assumed, then real nitrification rates may be much higher.

“We may be underestimating nitrification rates in the vast, nutrient-poor ocean,” noted study co-author Hannah Marchant.

Tracking single cells directly

To confirm the behavior of each group, the researchers needed tools that could distinguish the two lineages under a microscope. Earlier molecular methods could not do this accurately.

The team designed new probes to label each group with precision. After testing the probes, the researchers paired them with NanoSIMS imaging. This method reveals which nitrogen source each single cell uses.

“The new probes allowed us to see who was doing what in mixed communities like those in the Black Sea,” said Stuehrenberg.

Once the team viewed the samples with NanoSIMS, the pattern became unmistakable.

Two distinct lifestyles

Nitrosopumilus absorbed ammonium whenever it was available and used urea only when ammonium dropped.

Nitrosopelagicus drew from both ammonium and urea at the same time and continued using urea even when ammonium remained present.

This combination of new probes and NanoSIMS delivered a level of detail that earlier studies lacked.

Instead of guessing from indirect measurements, the team watched each group’s activity directly. That shift allowed the researchers to confirm two distinct lifestyles.

Broader implications for ocean microbes

Ammonia-oxidizing archaea are not minor members of the ocean community. They appear in huge numbers across the planet.

Nitrosopelagicus, in particular, dominates vast stretches of open water. Its ability to use urea and perhaps other organic nitrogen forms has major consequences for marine life.

Nitrogen availability influences primary production, plankton growth, and the movement of carbon through the ocean.

“Understanding what fuels these microorganisms is crucial,” said study co-author Marcel Kuypers. “They are major players in nitrogen cycling, and their activity helps regulate the nutrient availability in the ocean and the global carbon budget.”

The study’s findings make this statement even more relevant. If urea supports more microbial growth than expected, then our current global models may need updates.

Future research directions

Open ocean regions once viewed as low-activity zones may in fact support continuous microbial processes powered by multiple nitrogen sources.

This insight also shifts future research priorities. Scientists may explore how other organic nitrogen compounds contribute to nitrification.

Many such compounds drift through ocean waters from plankton, fish waste, sinking particles, and dissolved organic matter.

If archaeal groups use these compounds efficiently, then the ocean’s nitrogen cycle may be far more dynamic and adaptable than earlier views suggested.

The study is published in the journal Nature Communications.

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