Researchers catalog the microbiome of US rivers

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 waterbodies, the microbiology of rivers is relatively understudied.

A Colorado State University-led team of scientists 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.

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 co-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.”

Participatory science on a large scale

In addition to unlocking new insight into river microorganisms, the research published this week also showcases how participatory science can be successfully executed on a large scale, Wrighton said.

Wrighton first considered the project in 2018, while attending a national Department of Energy research meeting in Washington, D.C. At the meeting, Wrighton met James Stegen, a PNNL earth scientist, and learned that Stegen and his colleague, Amy Goldman, were already overseeing a massive, worldwide river sampling effort known as the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems, or WHONDRS. The program enlisted both scientists and non-scientists to collect river samples locally and send the samples to PNNL for analysis. Wrighton realized those same samples could also be analyzed for microbial data.

“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. We’re already working on a similar approach with wetlands.”

Stegen is excited by the results and the possibilities for new research to flow out of this work. “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.”

One of the keys in opening this work to a broader audience, Borton said, was to make the information accessible in a user-friendly database. To accomplish that, Borton turned to CSU Associate Professor Matt Ross, an ecosystem scientist who works with data analytics. Ross’ lab helped build the river microbiome data into a searchable, web-friendly platform.

“I’m really proud of the data accessibility part of this project,” Borton said.

Ross, a co-author on the paper, also helped Borton contextualize the data for the paper’s final analysis. He was somewhat surprised that granular microbial data connected so well to longstanding theories about big river ecosystems. “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. “This work aligns quite well with these old theories.”

In addition to being impacted by land use, river microbes were affected by other variables such as the size of the river, how much light hit the water surface, air temperature and the speed of the water flowing in the river. Those same factors also impact larger river species. What’s more, these factors were predictive of what microbes the researchers found, regardless of where in the U.S. the river was located. In fact, the team found six microbes in particular that were present and active in each of the roughly 100 rivers they studied. All six of those core microorganisms used light as an energy source.

“Microbes are active in these systems in such a way that is predictable across the continental U.S.,” Borton said. “I thought that we would find similar organisms in these different river systems, but I didn’t think the microbes would follow the tenets of these old river concepts for macro-organisms. That’s very cool, and I think says a lot about the robustness of the science that was done prior to our work.”

Borton hopes non-microbiome scientists will start using the data infrastructure they’ve built around river microbiomes, including incorporating microbial processes into efforts to better model ecosystems on a large scale. “We need to be better at studying across landscapes,” Borton said, “and better understanding rivers can help us do that.”