Rivers and streams are lifelines of ecosystems, connecting distant landscapes and influencing human health, agriculture, and energy production. They also provide two-thirds of the drinking water in the United States. Despite their significance, the microbiology of rivers remains understudied compared to larger water bodies.
A team led by Colorado State University (CSU) has taken strides to address this gap, producing the first comprehensive catalog of microorganisms in rivers spanning 90% of the continental U.S. watersheds. Published in Nature, this study marks a major advancement in understanding river microbiomes.
Rivers as Dynamic Ecosystems
The research underscores the critical role microbes play in river health. The paper's authors describe river microbes as "master orchestrators of nutrient and energy flows that will likely dictate water quality under current and future water scenarios."
The study highlights how these microbes interact with contaminants such as antibiotics, fertilizers, microplastics, and disinfection products. Notably, microbes near wastewater treatment plants expressed high levels of antibiotic resistance genes. Additionally, river microbes demonstrated the ability to break down microplastics into smaller carbon compounds.
Supporting the River Continuum Concept
Findings from the research bolster the decades-old River Continuum Concept, which views rivers as integrated systems where changes upstream affect downstream environments. This interconnectedness also applies to river microorganisms.
"People used to think of rivers almost just as pipes, a way to move water from one place to another," said Mikayla Borton, lead author and CSU research professor. "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."
A Massive Participatory Science Effort
The study cataloged over 2,000 microbial genomes from nearly 100 North American rivers. Most samples were collected by local community members through the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS), a program led by the Pacific Northwest National Laboratory (PNNL) in Washington state.
Kelly Wrighton, a professor at CSU and co-author, noted how the study demonstrates the strong relationship between human activity and microbial DNA in rivers. "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," she said.
A Template for Addressing Global Issues
This large-scale participatory research offers a blueprint for tackling global challenges like climate change. Wrighton explained that the success of this effort could inspire similar approaches in other ecosystems, such as wetlands.
"This is new frontier kind of stuff; we're really opening the doors to a deeply under-characterized part of the Earth," said James Stegen, a PNNL earth scientist and collaborator.
Data Accessibility for Future Research
To ensure the research's broader impact, the team built a searchable, web-based platform to house the river microbiome data. CSU Associate Professor Matt Ross, who led this effort, said he was "really proud of the data accessibility part of this project."
The study's findings also connect microbial activity to established ecological theories. "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," Ross said.
Predictable Patterns in Microbial Activity
The researchers identified six core microorganisms present in all studied rivers, demonstrating a predictable pattern of microbial activity across diverse environments. These microbes, which use light as an energy source, were influenced by factors like river size, light exposure, air temperature, and water flow speed—variables that also affect larger species.
"Microbes are active in these systems in such a way that is predictable across the continental U.S.," Borton said.
The findings pave the way for integrating microbial processes into large-scale ecosystem models. "We need to be better at studying across landscapes," Borton concluded, "and better understanding rivers can help us do that."
