Microbes play a big role in shaping the health of rivers

Rivers and streams act as vital lifelines, weaving through diverse landscapes, from secluded headwaters to vast oceans. 

These waterways play an essential role in human and environmental health, agriculture, and energy production, providing two-thirds of the United States’ drinking water. 

Yet, compared to larger water bodies like oceans and lakes, the microbiology of rivers has remained largely underexplored.

A team of scientists led by Colorado State University (CSU) has changed that. For the first time, they have cataloged the microorganisms present in rivers spanning 90% of the watersheds in the continental U.S., detailing their roles and functions. 

The findings, published in the journal Nature, highlight how river microbes influence nutrient flow, water quality, and even environmental health, opening a new frontier in microbiome research.

The essential role of river microbes

The study underscores the critical role of microbes in maintaining river health. According to the research, these microorganisms act as “master orchestrators of nutrient and energy flows,” playing a significant role in determining water quality under current and future conditions. 

The study also revealed how river microbes interact with contaminants like antibiotics, fertilizers, microplastics, and disinfection byproducts.

Notably, river microbes can degrade microplastics into smaller carbon compounds. However, near wastewater treatment plants, they exhibit high levels of antibiotic resistance genes, pointing to human impacts on these ecosystems. 

“People used to think of rivers almost just as pipes, a way to move water from one place to another,” said CSU research professor Mikayla Borton, the study’s lead author. 

“But rivers are much more than that – they’re performing all kinds of activities. And there’s a pattern to it; those activities can be predicted. Now, we know what microbes are performing some of those activities.”

Rivers as integrated systems 

The research also lends new support to the River Continuum Concept, a decades-old theory that views rivers as integrated systems where changes upstream directly affect downstream ecosystems. 

For instance, the health of a fish population at one point in a river depends on what happens upstream. The researchers found this interconnectedness also applies to microorganisms.

“One of the key ideas from the paper was that this tied back to river theory – how rivers change from small creeks to really large rivers. This work aligns quite well with these old theories,” said co-author Matt Ross, an associate professor at CSU.

Mapping river microbiomes across the U.S.

To catalog river microorganisms, the researchers analyzed over 2,000 microbial genomes from about 100 rivers across North America. 

The project relied heavily on community participation, with local volunteers collecting water samples through a program run by the Pacific Northwest National Laboratory (PNNL). These samples were then analyzed for microbial content.

Kelly Wrighton is a professor in CSU’s College of Agricultural Sciences and a co-author of the study. 

“When we look at how the land around a river is managed, we can see the processing of certain kinds of anthropogenic contaminants or chemicals through the microbes in their DNA,” said Professor Wrighton.

“There’s a very strong relationship – it suggests there’s a signal in the microbiome of how we’re living on and managing the land that is perpetuated into the river system and then downstream.”

Microbes as indicators of river health

Microbiome science is an emerging field with promising implications for environmental health. River microbes could serve as early-warning indicators of ecosystem changes, much like a canary in a coal mine. 

“Our hope is that this information can eventually be used to develop new diagnostics that are indicators of a healthy river versus an unhealthy river,” Wrighton explained. 

These insights could help scientists and policymakers better manage river systems and the landscapes surrounding them.

The research also uncovered six core microorganisms present in all rivers studied. These microbes, which use light as an energy source, were found to be active and predictable across the continental U.S. 

“Microbes are active in these systems in such a way that is predictable across the continental U.S.,” said Borton. “That’s very cool, and I think it says a lot about the robustness of the science that was done prior to our work.”

Tackling the world’s biggest problems

The study not only revealed new insights into river microbes but also showcased the potential of large-scale participatory science. 

The project began in 2018 when Wrighton met James Stegen, a PNNL earth scientist, who was already leading a global river sampling initiative. 

Wrighton realized that the samples collected for chemical analysis could also be studied for microbial data, launching a groundbreaking collaboration.

“There’s a lot of interest in mapping microbiomes, and there was this huge absence of microbial river data,” Wrighton said. 

“But I was also thinking, ‘Can we do this science at scale?’ Because if we can do science like this, if we can demonstrate that it works, we can tackle the world’s big problems like climate change. We could take this and apply it everywhere.”

User-friendly database of river microbiomes

One of the project’s key achievements was creating a searchable, user-friendly database of river microbiome data. 

Ross, an ecosystem scientist specializing in data analytics, helped build this platform and contextualize the findings for the study’s final analysis. “I’m really proud of the data accessibility part of this project,” Borton noted.

Borton hopes that the data infrastructure will inspire non-microbiome scientists to incorporate microbial processes into broader ecosystem models. “We need to be better at studying across landscapes, and better understanding rivers can help us do that,” Borton said.

New frontier for environmental science

This study opens the door to new research and practical applications. From tackling climate change to improving ecosystem modeling, the insights gained from river microbiomes could inform solutions to some of the world’s most pressing challenges. 

“This is new frontier kind of stuff; we’re really opening the doors to a deeply under-characterized part of the Earth,” Stegen said. “It is extremely gratifying to have built something that will benefit a lot of folks beyond our team.”

By revealing the hidden dynamics of river microbes, this research redefines how we understand rivers – not as mere conduits for water but as vibrant, interconnected ecosystems shaped by the smallest forms of life.

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