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Rivers and streams serve as vital arteries that connect diverse geographical areas, beginning in secluded headwaters and flowing vast distances toward oceans and deep seas. These waterways significantly influence human well-being, environmental health, agricultural productivity, and energy generation, supplying around two-thirds of the drinking water across the United States. Despite their importance, the microbiological aspects of rivers remain considerably less explored compared to larger bodies of water.
A research team led by Colorado State University (CSU) is aiming to change this landscape. They have published a groundbreaking study that unveils both the extensive and nuanced roles played by microorganisms in rivers, documenting their presence and functions across 90% of the watersheds in the continental U.S. This research, the result of a multi-year participatory science initiative, is featured in the journal Nature.
The findings reveal that microorganisms are crucial in maintaining the health of river ecosystems. The authors characterize these microbes as “master orchestrators of nutrient and energy flows” that can significantly influence water quality, particularly as environmental conditions evolve. Additionally, the research highlights the interaction between these microbes and contaminants in the water, underscoring the effects of human-made substances like antibiotics, disinfectants, fluorinated chemicals, fertilizers, and microplastics on river health. Remarkably, certain river microbes have demonstrated the ability to break down microplastics into smaller carbon compounds, while those near wastewater treatment facilities showed elevated levels of antibiotic resistance genes.
The study also substantiates a well-established ecological theory known as the River Continuum Concept, which perceives rivers as integrated systems where upstream conditions directly affect those downstream. This interconnectedness is mirrored in the behaviors of the microorganisms inhabiting these waterways.
“Traditionally, rivers were viewed merely as conduits for water transportation,” stated CSU Research Professor Mikayla Borton, the lead author of the Nature paper. “Our findings reveal that rivers perform a myriad of functions and that their activities can be anticipated. We now better understand which microbes are responsible for these processes.”
The research encompassed the analysis of over 2,000 microbial genomes from around 100 rivers throughout North America. Most of the data were derived from water samples collected by local residents through a river sampling initiative managed by the Pacific Northwest National Laboratory (PNNL), a research entity focusing on environmental and physical sciences under the auspices of the U.S. Department of Energy.
“Examining land management practices surrounding rivers allows us to trace how specific anthropogenic pollutants are processed by microbial DNA,” explained Kelly Wrighton, a co-author and professor in CSU’s College of Agricultural Sciences. “This connection indicates a clear signal in the river microbiome reflecting our land use practices and their impacts downstream.”
The branch of microbiome science continues to grow, with researchers optimistic about its potential applications. Microbes may serve as indicators—akin to a “canary in a coal mine”—for gauging the health of ecosystems, including rivers. “Our objective,” remarked Wrighton, a leader within CSU’s Microbiome Network, “is to leverage this research to develop diagnostics that can effectively distinguish between healthy and unhealthy rivers.”
Participatory Science at a Grand Scale
In addition to yielding novel insights about river microorganisms, this research illustrates the viability of conducting participatory science on a large scale, according to Wrighton.
The inspiration for this project originated in 2018 during a national Department of Energy meeting in Washington, D.C., where Wrighton met James Stegen, a PNNL earth scientist leading a globally coordinated river sampling program, called the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS). This program encouraged collaboration between scientists and the public to gather river samples for analysis at PNNL. Recognizing the opportunity, Wrighton proposed that these samples could also be analyzed for microbial composition.
“There is a burgeoning interest in mapping microbiomes, yet a void in microbial river data exists,” Wrighton noted. “We wondered if we could implement this type of science on a large scale to address significant global challenges like climate change. We are currently exploring a similar approach with wetlands.”
Stegen expressed enthusiasm about the new findings and the future research avenues they may usher in. “This is groundbreaking work; we are venturing into a significantly underexplored area of Earth science,” he commented. “It is satisfying to develop something that has broader implications beyond our immediate team.”
One pivotal aspect of this project was making the data accessible to a broader audience, which Borton emphasized. Collaborating with CSU Associate Professor Matt Ross, an expert in ecosystem science and data analytics, the team developed a searchable, web-friendly platform to facilitate access to the river microbiome data.
“I take great pride in the data accessibility component of this project,” Borton remarked.
Ross, also a co-author, played a significant role in contextualizing and analyzing the microbial data. He expressed surprise at how well the findings aligned with established ecological theories about river ecosystems. “A key takeaway from the paper is how these microbial patterns reflect known river dynamics—from small streams to large rivers,” Ross observed. “This alignment with classic river theories is quite compelling.”
Beyond the influence of land usage, the study found that river microbes were also impacted by variables such as river size, sunlight exposure, air temperature, and water flow speed—factors that also affect larger river organisms. The consistency of these factors across U.S. rivers allowed the researchers to identify six core microbial species that were prevalent and active in all studied rivers, with these microorganisms utilizing light as their primary energy source.
“These microbes exhibit predictable activity patterns across U.S. river systems,” Borton noted. “I anticipated finding similar organisms, but I did not expect them to adhere so closely to established theories for larger river species. This reinforces the robustness of prior ecological research.”
Borton hopes that researchers beyond the field of microbiome studies will utilize the data infrastructure developed for the river microbiome, particularly in modeling ecosystems more effectively. “We need to enhance our understanding of interconnected landscapes,” she asserted, “and advancing our knowledge about rivers is integral to achieving that goal.”
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