U.S. Department of Energy

Pacific Northwest National Laboratory

From Inundation Histories, a Conceptual Model Linking Hydrologic Fluctuations to Microbial Adaption and Biogeochemical Function

Fungi (branching organisms) perform well (green) and increase in non-inundated conditions, but are metabolically suppressed (orange) upon re-inundation by the river (blue shading), leading to lower CO2 flux (thin arrow). They propose that prolonged inundation shifts the community towards bacterial (rod-shapes) dominance. The influence of inundation history on the timescale of the transient, metabolically suppressed state is unknown.

The Science                      

River corridors exist worldwide and are comprised of multiple interacting components, all of them significant for their influences on biogeochemical cycling and microbial interactions. For example, the fluvial zone is the river itself, which strongly influences transport of materials, and the hyporheic zone is a very biogeochemically active subsurface region where groundwater and river water mix.

The less-studied parafluvial hyporheic zone is along river banks that are dry during low-flow conditions. It represents a critical interface between terrestrial and aquatic systems and understanding its dynamic hydrobiogeochemical behavior is fundamental for creating integrated models of dynamic river corridors. 

A new paper online in Biogeosciences Discussions, written by Amy E. Goldman and colleagues at the Pacific Northwest National Laboratory, uses inundation histories to fill in knowledge gaps in the biogeochemical cycling dynamics of the parafluvial hyporheic zone. The authors present a conceptual model of the irregular hydrologic fluctuations that are important to understanding the rapid cycles of wetting and drying in an increasing number of dam-controlled watersheds across the world, and the effect such cycles have on fluxes of CO2respiration.

The Impact

The new study is a first step towards extending reactive transport models by integrating the parafluvial hyporheic zone as a distinct environment within hydrobiogeochemical models. Capturing the processes that drive dynamics in this zone would provide more robust predictions of river corridor biogeochemical function under altered water flow regimes in both managed and natural watersheds. 


The parafluvial hyporheic zone, located in the region of the river channel that is dry during low flows, presents an important location for scientists to investigate biogeochemical cycling. Such zones impacted by dams are globally ubiquitous, and are likely to expand in number as the appetite for renewable energy rises across the world. That makes it important to identify the processes impacted by the history of variable river inundation.

In both controlled and natural riverine systems, however, the parafluvial hyporheic zone combines the prominent interactions of a hyporheic region with direct atmospheric-terrestrial inputs and the effects of wet-dry cycles. Because all river systems have parafluvial zones, understanding biogeochemical cycling and microbial interactions in this ecotone would further the understanding of how aquatic and terrestrial biogeochemical cycles are coupled.

The Goldman team characterized differences in biogeochemical and microbial variables present in the sediments of a representative parafluvial hyporheic zone along the Columbia River in southeastern Washington State. They collected samples along transects perpendicular to flow that spanned a continuum of inundation histories. At the extremes were samples inundated at the time of sampling and samples that had not been inundated for over 1 year. Results indicated that a combination of ecological and physiological mechanisms impeded the ability of the microbial communities to rapidly adapt to an inundated state. 

They found that inundation history influences the ability of parafluvial hyporheic microbial communities to respond to re-inundation, making this an important ecotone for understanding biogeochemical dynamics. The authors call for integrating the zone as a distinct environment within hydrobiogeochemical models in order to predict watershed biogeochemical function. 

They say future research is needed to investigate more ecologically and physiologically relevant causes for delays in microbial adaption and associated biogeochemical function, including the response to changes in the timing and magnitude of flow variation.

In both dam-impacted watersheds and in those projected to shift from snowpack-driven hydrology to rain-driven hydrology, there is a greater need for predicting biogeochemical responses to changes in inundation dynamics. 


This research was supported by the U.S. Department of Energy, Office of Biological and Environmental Research, as part of Subsurface Biogeochemical Research Program’s Scientific Focus Area at the Pacific Northwest National Laboratory.   


A.E. Goldman, et al., “Carbon cycling at the aquatic-terrestrial interface is linked to parafluvial hyporheic zone inundation history.” Biogeosciences Discuss., https://doi.org/10.5194/bg-2017-28. In review, 2017.

September 2017
| Pacific Northwest National Laboratory