Positive Interactions Dominate Among Marine Microbes, Six-Year Study Reveals

A six-year analysis of marine microbes in coastal California waters has overturned long-held assumptions about how the ocean's smallest organisms interact. 

Researchers at UC San Diego’s Scripps Institution of Oceanography found that marine microbes interact in ways that benefit one another more often than they eat each other or compete. The team also found that periods of elevated ocean temperatures, usually times of stress for these microbes because of a dearth of nutrients, actually resulted in even more of these positive interactions.

The study was published Jan. 21 in the ISME Journal: Multidisciplinary Journal of Microbial Ecology and was supported by the Simons Foundation, the National Science Foundation and NOAA. 

Marine microbes like bacteria and phytoplankton form the foundation of ocean food webs, providing sustenance for creatures ranging from zooplankton to whales and supporting fisheries that feed billions of people. These organisms also help regulate Earth's climate by cycling carbon, oxygen and nitrogen through the ocean and atmosphere. Yet, while ecologists have spent decades documenting how wolves, sea otters and other large animals interact in their ecosystems, the relationships among the ocean's most abundant life forms have received far less attention, creating a significant gap in our understanding of how marine ecosystems function.

The research team set out to answer three questions: How frequently and strongly do marine microbes interact? Are there keystone microbes that disproportionately influence their communities like sea otters? And does ocean temperature affect these interactions?

To find answers, the researchers relied on a unique dataset created by analyzing seawater samples that have been collected twice weekly from Scripps Pier in San Diego since 2018 by the Scripps Ecological Observatory and Southern California Coastal Ocean Observing System (SCCOOS). The power of this dataset comes from its long time series and the fact that it provides a way to observe marine microbial interactions in the ocean, while most prior research on this topic took place in the lab.

“Scripps Pier has an amazing history of long-term observations, most famously temperature. This time series adds to that legacy by giving us a long-term view of the entire microbial community in these samples,” said Jeff Bowman, a microbiologist at Scripps who started the data collection project with his students in 2018. “Scripps Pier is also unique in that the water we collect there is very similar to the seawater five miles offshore. Being able to get open ocean data without a ship is huge.” 

Using DNA sequencing, the team identified the microbes present in samples collected from 2018-2023, ultimately tracking 162 of the most abundant types. The researchers then applied computational methods to detect patterns in the data, revealing when changes in one organism's abundance caused changes in another's — as opposed to cases where organisms are simply responding to the same environmental factors.

The analysis revealed three surprising findings. First, positive interactions — where one microbe's growth promoted another's — were much more common than negative interactions like competition or predation. Roughly 78% of microbes had a net positive effect on their neighbors. The study didn’t reveal the mechanisms behind these positive interactions, but Ewa Merz, a postdoctoral researcher at Scripps and the study’s lead author, said a potential example could be one organism releasing waste that another species uses as nutrients. 

Second, the team found that there were indeed keystone microbes that interacted more with others in their community, making them more influential on the community’s structure. Third, temperature dramatically altered the way the organisms interacted. Across the 13°C (23°F) temperature range observed during the study, microbial communities became 33% less interactive in warmer conditions while shifting 11% towards more positive interactions. Interestingly, the identity of keystone microbial species changed with temperature.

“Marine ecologists have focused on competitive and predatory interactions while neglecting positive interactions," said Andrew Barton, a marine ecologist at Scripps and the study’s senior author. “Our results show that these positive interactions are common and underappreciated.” 

The findings suggest that warming oceans may do more than shift which microbes live where — it could fundamentally alter how marine microbial communities interact and function. Current ocean ecosystem models typically emphasize negative interactions like competition and predation while overlooking facilitation, and they don’t explicitly account for how interactions change with environmental conditions. This means predictions of how ocean ecosystems will respond to warming may be missing critical dynamics. Because marine microbes regulate carbon sequestration and support the fisheries that humanity depends on, these unseen shifts could have far-reaching consequences.

The authors recommend that future microbial community models incorporate positive interactions and seek to account for how relationships between species may vary with environmental conditions. They also note that their approach — pairing long-term, high-frequency sampling with computational methods — could be applied to microbial communities in other contexts such as soil or even the human gut to reveal similarly hidden dynamics. As ocean temperatures continue to rise, understanding how the microscopic foundation of marine life responds will be essential for anticipating changes to the ecosystems and services that depend on it.

In addition to Merz, Bowman and Barton, the study’s co-authors include Riley Hale, Erik Saberski, Kasia Kenitz and Melissa Carter of Scripps Oceanography and SCCOOS.