U.S. Department of Energy

Pacific Northwest National Laboratory

For the Hyporheic Zone, a Novel Thermodynamic Mechanism

Researchers working with James Stegen install monitoring gear in a hyporheic zone along the Columbia River.

The Science

Hyporheic zones are found within river corridor ecosystems across the world, and represent a dynamic continuum where groundwater (GW) and river water (RW) mix, stimulating biogeochemical activity. This activity has strong influences over the transformation of organic matter, nutrients, and contaminants, such as the conversion of dissolved organic carbon (DOC) to carbon dioxide (CO2). Such GW-RW mixing accounts for up to 95 percent of these transformations within the coupled river-subsurface component of river corridors.

 “River corridor” describes the broader system that includes the river, the surrounding landscape and vegetation, and the subsurface domain that interacts with the river. The “hyporheic zone” is a critical component of the river corridor.

Hyporheic zones are ecologically and biogeochemically consequential, but the mechanisms that stimulate their biogeochemical activity are poorly understood. 

A new Nature Communicationspaper, written by authors largely from the Pacific Northwest National Laboratory (PNNL), proposes a novel four-part thermodynamic mechanism that could underlie stimulated biogeochemical activity in the hyporheic zone—a mechanism that the authors say also has broader impacts on DOC and on microbial ecology.

The Impact

The new paper improves our understanding of the mechanisms governing DOC transformations and provides a new conceptualization for the role of thermodynamics. Its findings also provide a way to customize modeling frameworks for these types of systems, and will ultimately lead to improved predictions of how ecosystems respond to environmental change.


To date, there is no full accounting of the mechanisms that prompt and control the biogeochemical impacts of GW-RW mixing—a fact that weakens the present utility of process-based models built to predict the impacts of environmental change on river corridor ecosystems. 

A key challenge to improving such models is linking fine-scale processes (such as microbial activity) with larger-scale phenomena (such as the seasonal or dam-controlled pulses of GW-RW mixing).

One mechanism commonly thought to enhance the biogeochemical impacts of GW-RW mixing activity is the joining of electron donors (organic carbon, for example) with electron acceptors (like oxygen), a phenomenon that results in the well-known phenomenon of biogeochemical “hotspots.” 

The new Nature Communicationspaper proposes an alternative, four-part mechanism that governs the impacts of GW-RW mixing:

  1. Individual molecules of DOC that are found in GW are each (by themselves) more thermodynamically favorable for microbial transformation to CO2.
  2. Low DOC concentrations in GW protect these thermodynamically favorable DOC molecules. Then low amount of total energy available suppresses microbial transformation of DOC, which also occurs in deep-sea environments.
  3. DOC in RW is at higher concentrations, but each DOC molecule is less thermodynamically favorable for microbial transformation. This lower favorability protects DOC molecules in RW from microbial use.
  1. GW-RW mixing stimulates the transformation of DOC to CO2by combining GW’s low-concentration, but more favorable DOC, with RW DOC that is higher-concentration but less favorable for microbial transformation.  

To arrive at these mechanisms, the research team sampled GW and RW from 10 wells, a near-shore piezometer, and the river itself for seven months along 400 meters of the Columbia River in the Hanford 300 area in southeastern Washington State.

Such thermodynamic mechanisms regulated by GW-RW mixing, previously unrecognized, may strongly influence biogeochemical and microbial dynamics in river corridor ecosystems.

These mechanisms are particularly relevant to systems like the Hanford Site where there is oxygen in both the river water and in the adjacent groundwater. In these types of systems, classic paradigms do not apply, undermining our ability to properly represent underlying mechanisms within predictive modeling frameworks.

The researchers observed that mixing removes the protection mechanisms for both GW and RW, but only across a narrow range of mixing conditions. If there is more than 10 percent GW, the stimulation is lost. At that level of GW contribution, the DOC concentration falls to a level that may be low enough that microbes cannot transform the DOC present there.

Intriguingly, the same concentration was found to limit microbial use of DOC in the deep sea, suggesting a universal mechanism could be at work. 

The idea that DOC transformations are regulated by a defined threshold, apparent in both the hyporheic zone and in the deep sea, could be a starting point for future experiments designed to reveal deeper mechanisms.

Meanwhile, the authors hypothesize that the more favorable DOC in GW may be related to elevated methane concentrations in sediments, as well as to leachate from buried organic carbon derived from deposits of woody material.

The authors tested their thermodynamics-based hypothesis using high-resolution profiles of DOC samples via Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) at the Environmental Molecular Sciences Laboratory, a U.S. Department of Energy science user facility located on the PNNL campus.

In turn, they used time-lapse electrical resistivity tomography (ERT) across the broader groundwater aquifer to examine the larger-scale implications of mixing-driven stimulation of DOC transformations. This was done using an array of 352 electrodes divided into 11 lines spaced about 25 meters apart.

This ERT array produced 4-dimensional images of changes in electrical conductivity throughout the aquifer. These images were translated into GW-RW mixing and DOC concentrations, and indicated that stimulated transformations of DOC due to GW-RW mixing prevented the penetration of DOC into the broader aquifer. This dynamic has significant effects on the biogeochemical function of the broader aquifer system.

Researchers also found further linkages between ecological drivers of microbiome composition and DOC biochemistry, which highlights critical feedbacks among hydrology, DOC biochemistry, and microbial ecology. 

In all, the paper provides a new thermodynamically-based conceptualization of how GW-RW mixing influences the biogeochemical function of hyporheic zones and groundwater aquifers, which are critical components of broader river corridor ecosystems.

Presently, the research team is building this new conceptualization into process-based models, which will be used to predict the impacts of environmental change on river corridor hydro-biogeochemistry.


J.C. Stegen, et al., “Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.” Nature Communications. volume 9, Article number: 585(2018) [doi:10.1038/s41467-018-02922-9]



February 2018
| Pacific Northwest National Laboratory