Study reveals how ocean's most abundant bacteria diversify

A groundbreaking study led by the University of Hawaiʻi at Mānoa's Hawaiʻi Institute of Marine Biology (HIMB) has revealed critical new details about one of the ocean's most abundant life forms, SAR11 marine bacteria. Understanding these microbes is vital because they are one of the main drivers of the global ocean's life-support system—they move and recycle the carbon and nutrients that sustain all other marine life. By better understanding them, scientists can more accurately predict how the entire ocean ecosystem—and the global climate—will react to threats like pollution and ocean warming.

The research, published in Nature Communications, found that the SAR11 bacteria are not a single, uniform population as often thought. Instead, they are organized into stable, ecologically distinct groups, essentially specialized "teams" adapted to specific environments, such as the coast versus the open ocean. This means that one of the ocean's most important engines is far more complex than previously known.

Using Kāneʻohe Bay as a natural laboratory, the team linked newly cultivated strains to ocean samples worldwide, showing that these distinct ecological groups differ significantly in habitat preference, gene content, and evolutionary history.

“Kāneʻohe Bay gave us a rare window into how microbial populations can adapt across very small spatial scales,” said Kelle Freel, lead author at HIMB. “By pairing cultivation with a long-term time series, we could directly connect genomes to real ecological differences in the ocean.”

SAR11 bacteria are tiny, streamlined cells that collectively represent one of the most abundant life forms in the ocean and play a central role in marine carbon and nutrient cycling. Despite their global importance, scientists have struggled to understand how SAR11 populations differ from one another, in part because these microbes are extremely diverse and very difficult to grow in the laboratory.

Kāneʻohe Bay provided a uniquely powerful model system to overcome these challenges. Years of sustained sampling through the Kāneʻohe Bay Time-series (KByT) allowed researchers to pair environmental measurements with newly grown SAR11 strains, creating an opportunity to connect microbial DNA with where these organisms live and how they survive.

“This work shows that SAR11 diversity is not random,” said Michael Rappé, principal investigator at HIMB. “By using Kāneʻohe Bay as a model system, we could integrate genomics with ecology in a way that reveals clear evolutionary structure - structure that holds across the global ocean and provides a common framework for studying one of the planet’s most important microbial groups.”

Ecologically distinct units

By culturing and sequencing the whole genomes of 81 new SAR11 isolates originating from coastal and offshore waters, the researchers tripled the number of complete genomes available for strains of this bacterial group. When these genomes were analyzed together with more than 1,300 marine metagenomes from oceans around the world, clear and repeatable ecological patterns emerged.

Rather than blending together as one large population, SAR11 bacteria consistently grouped into ecologically distinct units, whose members shared similar habitats and biological traits across space and time. 

A related study published in The ISME Journal revealed that whether SAR11 bacteria thrive near the coast or in the open ocean around Kāneʻohe Bay can depend on just a small number of genes under strong environmental selection. 

These findings show how small genetic differences can lead to significant ecological differences, helping explain how SAR11 maintains diversity despite large population sizes and global dispersal.