U.S. Department of Energy

Pacific Northwest National Laboratory

Coupling spatiotemporal community assembly processes to changes in microbial metabolism

The Columbia River.

The Science                               

Ecological processes govern seasonal changes in microbial communities living along rivers in the hyporheic zone, where groundwater and surface water mix. These processes have been well-studied in plant and animal communities. But the extent to which they govern riverine microorganisms that regulate ecosystem carbon and nutrient availability is unknown.

Global temperatures continue to rise. Changes in land use continue to alter nutrient inputs into river systems. So knowing more about hyporheic carbon and nutrient cycling is important for protecting ecosystems and human health.

Scientists studying the hyporheic zone typically just analyze the complex conditions in either groundwater or river water. Focusing instead on where the two types of water mix is incredibly challenging. But it is critical for understanding the planet’s response to environmental change.

The Impact

New technology, along with advances in statistical modeling approaches developed at the Pacific Northwest National Laboratory (PNNL), now allow for the investigation of these hyporheic zone dynamics across space and time in microbial communities.

Bacteria, fungi, algae, and other microorganisms in and around rivers worldwide convert massive amounts of organic carbon into carbon dioxide. Yet scientists understand little about how organisms change through space and over time or what processes drive these changes. 

The results in this paper will help researchers understand the mechanisms that drive increases and decreases in organisms that produce pollutants and greenhouse gases.


The hyporheic zone is a critical ecological feature. It harbors a rich diversity of microorganisms that regulate carbon and nutrient availability for other organisms along the river. Hyporheic microorganisms can remove excess nutrients from agricultural and sewage run-off. They can also release carbon dioxide into the atmosphere by processing organic matter from inland and upriver plant debris.

In the current study, PNNL researchers aim for two outcomes: a mechanistic basis for describing the current state of such riverine ecosystems and a means of predicting how they will change in response to future environmental scenarios. 

From their river field site, researchers gathered sophisticated measurements every three weeks to describe microorganisms and chemistry in the Columbia River and its hyporheic zone. They also used newly developed statistical modeling approaches pioneered at PNNL to infer ecological processes through space and time. The team conducted its study from March to November 2014. Their field site was in central Washington, where the Columbia, one of the nation’s largest rivers, flows near the Hanford site, a former nuclear materials processing facility. 

The researchers are working to incorporate mechanistic information on microbial communities into Earth Systems Models. This will help better predict rates of carbon and nitrogen cycling in future climates.


Office of Biological and Environmental Research (BER) as part of Subsurface Biogeochemistry Research Program’s Scientific Focus Area (SFA) at the Pacific Northwest National Laboratory (PNNL).


E. Graham, Crump AR, Resch CT, Fansler S, Arntzen E, Kennedy D, Fredrickson J, Stegen JC. (2016) “Coupling spatiotemporal community assembly processes to changes in microbial metabolism.” Frontiers in Microbiology. DOI: 10.3389/fmicb.2016.01949

December 2016
| Pacific Northwest National Laboratory