As sea levels rise due to climate change, encroaching seawater will likely make freshwater environments saltier. In a new study, MIT researchers have shown how that increase in salinity might affect microbial ecosystems found in environments such as rivers and estuaries.
These microbial communities play important roles in the carbon cycle, and they also help decompose organic matter such as algae. The MIT team found that when salt levels rise, these populations lose diversity as faster-growing strains tend to take over the community, but they maintain their overall growth rate.
"At higher salinity, you lose diversity, which is ultimately not good for an ecosystem. But what we were surprised at is that in the meantime, even though diversity decreases, the growth of the community and the production of biomass is not impacted that much," says Jana Huisman, an MIT postdoctoral researcher and the lead author of the new study.
Jeff Gore, an MIT professor of physics, is the senior author of the paper, which appears in Nature Microbiology. Martina Dal Bello, a former MIT postdoctoral researcher who is now an assistant professor of ecology and evolutionary biology at Yale University, is also an author of the study.
Rising salt levels
Microbes that live in aquatic environments are typically adapted to thrive in freshwater or saltwater, or somewhere in between. Microbes that live in higher-salt environments have cell walls that are optimized to resist osmotic pressure and membrane transporters that can pump sodium ions out of the cell.
Freshwater lakes and rivers have salt concentrations around 1 gram of salt per liter of water (g/L), while oceans can reach 35 g/L. As the climate warms and sea levels rise, those ocean waters may seep into estuaries and other inland bodies of water, increasing their salinity.
"When you think about climate change, you can think about rising temperatures, which is very common, but also a lot of other environmental stresses are going to increase," Huisman says.
Huisman is from the Netherlands, a country with an extensive coastal delta, and she was interested in exploring how changes in salinity might affect microbial ecosystems in those aquatic habitats. The new study builds on previous work from Gore's lab showing that higher seawater temperatures tend to favor slower-growing bacteria.
For the new study, the researchers took samples from three aquatic environments with varying salinity: the Charles River near the MIT Sailing Pavilion (4 g/L), Boston Harbor (30 g/L) and a beach in Nahant, Massachusetts (35 g/L). Each community contained hundreds of species of microbes. The researchers then grew each population in three environments of varying salinity—16, 31 or 46 g/L.
Over two weeks, the researchers measured the communities' growth rates and found that each community maintained the same growth rate at each of the three concentrations. However, in the communities exposed to higher-salt environments, the overall composition became less diverse. Further studies showed that these communities tended to be dominated by faster-growing species.
"We saw that those communities that had been propagated at higher salinity had reached a markedly different composition than the ones at lower salinity," Huisman says.
Natural ecosystems
To explore whether their lab results might correspond to what happens in natural ecosystems, the researchers analyzed publicly available genomic data from microbes found in different aquatic ecosystems, including the Chesapeake Bay, the Gulf of Mexico and the Baltic Sea.
For this portion of the study, the researchers focused on a genetic marker called the 16S rRNA gene copy number, which can be used as a proxy for the maximum growth rate that a species can attain. The more copies of this gene that a species has, the faster its intrinsic growth rate.
The researchers found that in these natural communities, environments with higher salinity also tended to be dominated by faster-growing species.
"When we first saw that, it was very exciting—that, indeed, what we found in the lab seems to also be represented in data from natural communities, sampled across a range of different environments," Huisman says. "You see the same signatures in such data, and that's highly suggestive that what we found in the lab might also be true in natural environments."
One potential drawback to this loss of diversity is a reduction in microbial populations' ability to withstand other types of environmental stress, the researchers say.
In this study, the researchers did not investigate the functions of the individual bacterial strains that ended up becoming more prevalent. Some of them may play beneficial roles, but it's also possible that some of them might be pathogenic strains.
"Whether you want faster-growing species to take over or not might also be related to the identity of those species. That is something that I'm interested in looking at in the future," Huisman says.
Publication details
Jana S. Huisman et al, Predictable shifts in microbial species composition lead to community-wide robustness to environmental stress, Nature Microbiology (2026). DOI: 10.1038/s41564-026-02422-3
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Citation: How an influx of salt may affect microbial ecosystems in rivers, estuaries and coastal waters worldwide (2026, July 17) retrieved 17 July 2026 from https://phys.org/news/2026-07-influx-salt-affect-microbial-ecosystems.html
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