Adapted from a news release by Colorado State University.

Rivers and streams serve as critical connectors across vast geographical landscapes, trickling out of tucked-away headwaters and snaking thousands of miles toward oceans and deep seas. These waterways directly impact human and environmental health, agriculture and energy production, and supply the United States with two-thirds of its drinking water. And yet, compared with other larger water bodies, the microbiology of rivers is relatively understudied.

A Colorado State University-led team of scientists including researchers from Lawrence Berkeley National Laboratory (Berkeley Lab) have contributed to changing that — detailing for the first time both broad and specific information about the presence and function of microorganisms in rivers covering 90% of the watersheds in the continental U.S. Cataloging the microbiome of these rivers is the result of a yearslong participatory science effort published this week in the journal Nature.

Berkeley Lab expertise and capabilities enabled this research by bringing genomic sequencing tools and expertise along with making the data widely accessible through public databases. “A project of this scale really demonstrates the power of open, distributed science to address big questions about how microbes impact ecosystem processes,” said Emiley Eloe-Fadrosh, head of the Metagenome Program at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility located at Berkeley Lab, and lead PI of the National Microbiome Data Collaborative (NMDC).

“A project of this scale really demonstrates the power of open, distributed science to address big questions about how microbes impact ecosystem processes.”

— Emiley Eloe-Fadrosh

This new research suggests that microbes play a significant role in shaping the overall health of rivers. 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.” What’s more, the authors found these microbes are interacting with contaminants found in the water, adding new detail to an existing body of evidence showing that rivers are impacted by artificial inputs such as antibiotics, disinfection products, fluorinated compounds, fertilizers, and microplastics. Notably, river microbes had the ability to degrade microplastics into smaller carbon compounds, and microbes found near wastewater treatment plants expressed high levels of antibiotic resistance genes.

The study also found that river microbe behavior supports a decades-old idea known as the River Continuum Concept — a macro-ecological theory that views rivers as one continuously integrated system. For example, a particular type of fish thriving at a particular spot in a river is inextricably linked to what’s happening upstream. Turns out, this is also true of river microorganisms.

“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, lead author on the Nature paper. “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.”

The study involved cataloging more than 2,000 microbial genomes from about 100 rivers across North America — a majority from water samples collected by local community members through a sampling program run by the Pacific Northwest National Laboratory, or PNNL, an environmental and physical sciences research lab located in Washington state and operated by Battelle, a private nonprofit, on behalf of the U.S. Department of Energy.

“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 Kelly Wrighton, a professor in CSU’s College of Agricultural Sciences and a senior author on the paper. “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.”

Microbiome science is an emerging scientific field. One of the key promises of this research area is that microbes can function as a kind of canary in the coal mine for the health of both humans and critical ecosystems — soils, oceans, or, say, the overall wellness of a river. “Our hope,” said Wrighton, one of the leaders of CSU’s Microbiome Network, an interdisciplinary research group, “is that this information can eventually be used to develop new diagnostics that are indicators of a healthy river versus an unhealthy river.”