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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Combined Effects of Stream Hydrology and Land Use on Basin‐Scale Hyporheic Zone Denitrification in the Columbia River Basin

Abstract Denitrification in the hyporheic zone (HZ) of river corridors is crucial to removing excess nitrogen in rivers from anthropogenic activities. However, previous modeling studies of the effectiveness of river corridors in removing excess nitrogen via denitrification were often limited to the reach‐scale and low‐order stream watersheds. We developed a basin‐scale river corridor model for the Columbia River Basin with random forest models to identify the dominant factors associated with the spatial variation of HZ denitrification. Our modeling results suggest that the combined effects of hydrologic variability in reaches and substrate availability influenced by land use are associated with the spatial variability of modeled HZ denitrification at the basin scale. Hyporheic exchange flux can explain most of spatial variation of denitrification amounts in reaches of different sizes, while among the reaches affected by different land uses, the combination of hyporheic exchange flux and stream dissolved organic carbon (DOC) concentration can explain the denitrification differences. Also, we can generalize that the most influential watershed and channel variables controlling denitrification variation are channel morphology parameters (median grain size (D50), stream slope), climate (annual precipitation and evapotranspiration), and stream DOC‐related parameters (percent of shrub area). The modeling framework in our study can serve as a valuable tool to identify the limiting factors in removing excess nitrogen pollution in large river basins where direct measurement is often infeasible.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Linkages Between Mineral Element Composition of Soils and Sediments With Hyporheic Zone Dissolved Organic Matter Chemistry Across the Contiguous United States

The hyporheic zone is a hotspot for biogeochemical cycling where interactions with mineral metals preserve the release and biodegradation of organic matter (OM). A small fraction of OM can still be exchanged between localized sediments and the overlying water column, and recent evidence suggests there exists a longitudinal structuring in sediment dissolved OM (DOM) chemistry across the continental United States (CONUS). In this study, we tested a hypothesis that water extractable sediment DOM chemistry could be explained by sediment metal contents and integrative watershed scale features at the CONUS scale. Crowdsourced samples were characterized for high resolution mass spectrometry and coupled with sediment metals determined via x-ray fluorescence as well as with land cover and soil elemental information obtained from national databases. Our results highlight weak relationships between DOM chemistry and elemental composition at the CONUS scale indicating limited transferability of organo-metal linkages into multi-scale hydrobiogeochemical models.

58 GEOSCIENCES↗
DOE OSTI2024

Mechanistic definition and prediction of the mass exchange coefficient between rivers and hyporheic zones: The $α$ of two $Ω$s

Solute transport in interconnected rivers and hyporheic zones is typically modeled through dual-domain models where first-order solute mass transfer between the two domains, Ω R and Ω HZ , is represented by a coefficient α. The transient storage model (TSM) is an example of such an approach. In practice, α is determined by fitting the tails of solute tracer breakthrough curves using a TSM. This approach has led to ambiguity regarding α’s physical meaning and transferability. Here, in this work, we investigated the physical basis for α and tested it with virtual experiments through the fully coupled multiphysics model hyporheicFoam for the Ω R – Ω HZ system. hyporheicFoam explicitly simulated coupled flow and solute transport over a kilometer with centimeter-scale resolution. Model results were analyzed to calculate α following its theoretical definition directly. Using the determined α within a TSM enables accurate reproduction of solute transport, underscoring α’s physical relevance and precision.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

FTICR-MS and Biochemical Transformation Data from Global Inland River Water and Sediment Associated with: "Organic Matter Transformations are Disconnected Between Surface Water and the Hyporheic Zone"

This data package is associated with the publication "Organic Matter Transformations are Disconnected Between Surface Water and the Hyporheic Zone" submitted to Biogeosciences (Stegen et al., 2022). The study aims to understand how the diversity of OM transformations varies across surface and subsurface components of river corridors using inland surface water and sediments collected along river corridors across the contiguous United States. Sediment extracts and water samples were analyzed using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). This dataset is comprised of one folder (WHONDR_S19S) which contains (1) a subfolder with R scripts used to process the data and to calculate biochemical transformations, (2) processed FTICR-MS data as csv files, sample collection metadata and climate data as csv files, (3) biochemical transformations profile, classifications and database as csv files, and (4) a readme file with more information regarding WHONDRS raw FTICR-MS data and processing scripts. Outside of the main folders there is a csv containing file-level metadata and a csv data dictionary defining column headers for all csv files contained in the data package. The samples were part of a WHONDRS (https://whondrs.pnnl.gov) study. The raw, unprocessed FTICR-MS data with additional data can be found at doi:10.15485/1729719 for sediments and doi:10.15485/1603775 for water. This data package contains the processed data used in the associated manuscript.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A multirate mass transfer model to represent the interaction of multicomponent biogeochemical processes between surface water and hyporheic zones (SWAT-MRMT-R 1.0)

Abstract. Surface water quality along river corridors can be modulated by hyporheic zones (HZs) that are ubiquitous and biogeochemically active. Watershed management practices often ignore the potentially important role of HZs as a natural reactor. To investigate the effect of hydrological exchange and biogeochemical processes on the fate of nutrients in surface water and HZs, a novel model, SWAT-MRMT-R, was developed coupling the Soil and Water Assessment Tool (SWAT) watershed model and the reaction module from a flow and reactive transport code (PFLOTRAN). SWAT-MRMT-R simulates concurrent nonlinear multicomponent biogeochemical reactions in both the channel water and its surrounding HZs, connecting the channel water and HZs through hyporheic exchanges using multirate mass transfer (MRMT) representation. Within the model, HZs are conceptualized as transient storage zones with distinguished exchange rates and residence times. The biogeochemical processes within HZs are different from those in the channel water. Hyporheic exchanges are modeled as multiple first-order mass transfers between the channel water and HZs. As a numerical example, SWAT-MRMT-R is applied to the Hanford Reach of the Columbia River, a large river in the United States, focusing on nitrate dynamics in the channel water. Major nitrate contaminants entering the Hanford Reach include those from the legacy waste, irrigation return flows (irrigation water that is not consumed by crops and runs off as point sources to the stream), and groundwater seepage resulting from irrigated agriculture. A two-step reaction sequence for denitrification and an aerobic respiration reaction is assumed to represent the biogeochemical transformations taking place within the HZs. The spatially variable hyporheic exchange rates and residence times in this example are estimated with the basin-scale Networks with EXchange and Subsurface Storage (NEXSS) model. Our simulation results show that (1), given a residence time distribution, how the exchange fluxes to HZs are approximated when using MRMT can significantly change the amount of nitrate consumption in HZs through denitrification and (2) source locations of nitrate have a different impact on surface water quality due to the spatially variable hyporheic exchanges.

58 GEOSCIENCES↗
DOE OSTI2020

A Flux Detection Probe to Quantify Dynamic Groundwater-Surface Water Exchange in the Hyporheic Zone

A new probe was designed to quantify groundwater-surface water exchange in the hyporheic zone under dynamic stage condition. Current methods focus on either vertical pore water velocity or Darcy flux measurements. Both parameters must be understood to evaluate residence time and mass flux of constituents. Furthermore, most instruments are not well suited for monitoring instantaneous velocity or flux under dynamic exchange conditions. For this reason, the flux detection probe (FDP) was designed that employs electrogeophysical measurements to estimate in situ sediment porosity, which can be used to convert pore water velocity to Darcy flux. Dynamic pore water velocity is obtained by monitoring fluid conductivity and temperature along the FDP probe. Pressure sensors deployed at the top and bottom of the probe provide the additional information necessary to estimate vertical permeability. This study focuses on the use of a geophysical method to estimate pore water velocity, porosity, and permeability within a controlled soil column where simulated river water displaces simulated groundwater. The difference between probe derived and theoretical pore water velocity using natural tracers such as electrical conductivity and temperature was -4.9 and 3.9% for downward flow and 1.1 and 12.8% for upward flow, respectively. The difference in porosity calculated from mass and volume packed in the soil column and probe measure porosity ranged between -3.2% and 1.5%. Also, the calculated hydraulic conductivity differed from probe derived values by -8.9%.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Hyporheic zone, river, and groundwater metagenome resolved genomes and rpS3 genes in East River Watershed, Colorado USA Summer 2020, 2021

Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from water filter collected across 8 locations along the East River Watershed, CO, and 1 nearby groundwater well. The purpose was to look for connectivity and similarities across the network and to see the impact of the groundwater. As a part of Lawrence Berkeley National Laboratory (LBNL) Watershed Science Focus Area (SFA), we assessed community composition and strain similarities between the sites and we also compared it to previous metagenomic studies within the watershed looking at floodplain (Matheus Carnevali et al. 2021) and hillslope (Lavy et al. 2019) microbiomes. Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from filters across 8 locations during August 2020 and July 2021. This resulted in 32 samples. The groundwater sample was sequenced at UC Berkley's QB3. The other 31 samples were sequenced at University of Maryland. Metagenomes were assembled using four autobinners and the best bins were selected using dasTool. The genomes were dereplicated at 95% with dRep and the subset of winning genomes were manually curated based on visual inspection of taxonomic profile, GC content, coverage, and a set of 51 bacterial single copy genes (BSCG), and 38 archaeal signal copy genes (ASCG). The dataset includes a zip file of 311 genomes (HZ_River_SW_MAGS_Dereplicated_95.zip). The dataset additionally includes a zipped file of ribosomal protein small subunit 3 (rpS3) proteins from the hyporheic zone and river data (rpS3_Proteins_HZ_River.zip), a metadata file used to register associated samples with IGSNs (International Generic Sample Numbers) (samples.csv), a location metadata file (locations.csv). This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

DNA↗
DOE OSTI2025

Hyporheic-zone Processes and Stream Oxygen Dynamics: Insights from a Multiscale Reactive Transport Model: Modeling Archive

This archive contains the data and Python scripts required to reproduce the analyses and figures in the study: Gomez-Velez, J. D., Rathore, S. S., Cohen, M. J., & Painter, S. L. (2025). Hyporheic-zone Processes and Stream Oxygen Dynamics: Insights from a Multiscale Reactive Transport Model. Submitted to Water Resources Research. The analysis utilizes the subgrid model Advection Dispersion Equation with Lagrangian Subgrids (ADELS) implemented in the Advanced Terrestrial Simulator (ATS; https://amanzi.github.io/ats/stable/). In this case, the ATS and Amanzi versions are (1) ATS version 1.5.1_f5ba18f8 and (2) Amanzi version 1.6-dev_53444cca4. The repository includes a Jupyter Notebook and the necessary data (Pandas DataFrames stored as pickle files) to generate the figures for the manuscript. Additionally, it contains Python scripts to create ATS input files, run the ATS simulations, and post-process the results. Finally, it provides routines for parameter estimation using the Single-Station Metabolism (SSM) model with the Differential Evolution Adaptive Metropolis (DREAM) Markov Chain Monte Carlo (MCMC) algorithm with ZS enhancements (DREAM-ZS).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Data From: Influence of Hydrological Perturbations and Riverbed Sediment Characteristics on Hyporheic Zone Respiration of CO2 and N-2, Journal of Geophysical Research-Biogeosciences

This data package contains pumping data (.txt), parameter matrices, and R code (.R, .RData) to perform bootstrapping for parameter selection for the bioclogging model development. The pumping data were collected from the Russian River Riverbank Filtration site located in Sonoma County, California from 2010-2017 from three riverbank collection wells located alongside the study site. The pumping data is directly correlated with water table oscillations, so the code performs these correlations and simulates stochastic versions of water table oscillations. See Metadata Description.pdf for full details on dataset production. This dataset must be used with the R programming language. This dataset and R code is associated with the publication "Influence of Hydrological Perturbations and Riverbed Sediment Characteristics on Hyporheic Zone Respiration of CO2 and N-2"This research was supported by the Jane Lewis Fellowship from the University of California, Berkeley, the Sonoma County Water Agency (SCWA), the Roy G. Post Foundation Scholarship, the U.S. Department of Energy, Office of Science Graduate Student Research (SCGSR) Program, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award DE-AC02-05CH11231, and the UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Organic matter transformations are disconnected between surface water and the hyporheic zone

Abstract. Biochemical transformations of organic matter (OM) are a primary driver of river corridor biogeochemistry, thereby modulating ecosystem processes at local to global scales. OM transformations are driven by diverse biotic and abiotic processes, but we lack knowledge of how the diversity of those processes varies across river corridors and across surface and subsurface components of river corridors. To fill this gap we quantified the number of putative biotic and abiotic transformations of organic molecules across diverse river corridors using ultra-high-resolution mass spectrometry. The number of unique transformations is used here as a proxy for the diversity of biochemical processes underlying observed profiles of organic molecules. For this, we use public data spanning the contiguous United States (ConUS) from the Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems (WHONDRS) consortium. Our results show that surface water OM had more biotic and abiotic transformations than OM from shallow hyporheic zone sediments (1–3 cm depth). We observed substantially more biotic than abiotic transformations, and the numbers of biotic and abiotic transformations were highly correlated with each other. We found no relationship between the number of transformations in surface water and sediments and no meaningful relationships with latitude, longitude, or climate. We also found that the composition of transformations in sediments was not linked with transformation composition in adjacent surface waters. We infer that OM transformations represented in surface water are an integrated signal of diverse processes occurring throughout the upstream catchment. In contrast, OM transformations in sediments likely reflect a narrower range of processes within the sampled volume. This indicates decoupling between the processes influencing surface water and sediment OM, despite the potential for hydrologic exchange to homogenize OM. We infer that the processes influencing OM transformations and the scales at which they operate diverge between surface water and sediments.

58 GEOSCIENCES↗
DOE OSTI2021

Bedrock architecture, soil texture, and hyporheic zone characterization combining electrical resistivity and induced polarization imaging

The shallow (<15 m depth) subsurface environment of a short reach along a bedrock stream was investigated with electrical resistivity and induced polarization (IP) to map details of bedrock and soil sediments. The bedrock is mostly comprised of limestone, and is generally resistive compared to the overlying soil. The soil-bedrock interface was determined through a trial and error approach using a sharp boundary feature in the inversion model. The inferred bedrock surface determined from the inversions exhibited undulating patterns with troughs and ridges. A near continuous trough ran alongside the stream within the floodplain, and is suggestive of a paleochannel among other interpretations of this feature. The structure of the electrical resistivity above the bedrock showed small-scale elongated features. The chargeability from the IP method showed larger scale features. High values of chargeability were associated with the sediments in the floodplain, and low values were associated with bedrock, stream, and soil on the elevated banks above the stream. If the chargeability is associated with membrane polarization characteristic of clayey soils, then IP seems to highlight the mere existence of clay, while the resistivity may be more discernable of the relative proportion of clay. Vegetation differences may also explain the chargeability distribution, where parts of the survey with high chargeability had dense pine with no understory making the soils more organically rich.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Hyporheic‐Zone Processes and Stream Oxygen Dynamics: Insights From a Multiscale Reactive Transport Model

Aquatic ecosystem metabolism encapsulates the daily fixation (gross primary production, GPP d ) and mineralization (ecosystem respiration, ER d ) of organic carbon. In fluvial systems, these are commonly estimated by inverse solutions to field observations using a model that describes oxygen concentrations varying in the water column in response to metabolic fluxes and air‐water gas exchange controlled by a rate coefficient (K 600 ). The most common conceptual model is the single‐station metabolism (SSM) model. The simplicity and flexibility of this conceptualization make it attractive; however, it implicitly assumes that all the processes that consume oxygen in fluvial systems can be lumped into a bulk estimate of respiration with poorly understood consequences for estimates of GPP d , ER d , and K 600 . Here, we focus on the implications of using SSM conceptualization when estimating metabolic fluxes from oxygen dynamics in channels where hyporheic exchange occurs. We use a new multiscale numerical model for reactive transport in streams that represents hyporheic exchange and streambed heterotrophic respiration. Nondimensionalization of this model reveals dimensionless groups that collectively control oxygen dynamics. Numerical experiments offer a mechanistic understanding of the impacts of hyporheic exchange on diel oxygen dynamics revealing that potential biases arise from neglecting mass transfer limitations. Specifically, we found that hyporheic exchange significantly affects diel oxygen dynamics, even for nonreactive streambed sediments. Moreover, while the SSM performs well in many situations, we find conditions where significant bias is produced by hyporheic exchange, even when oxygen data are well‐fitted. These situations pose a major challenge in the interpretation of metabolism assessment estimates.

Gomez‐Velez, Jesus D. [Oak Ridge National Laborato↗
DOE OSTI2024

Trace Metal Dynamics and Limitations on Biogeochemical Cycling in Wetland Soils and Hyporheic Zones

Biogeochemical cycling in subsurface aquatic systems is driven by anaerobic microbial processes that employ metalloenzymes. Pure culture studies reveal that low availability of trace metals may inhibit methanogenesis, mercury methylation, and reduction of N 2 O to N 2 during denitrification. However, whether such limitations occur in natural subsurface aquatic systems is currently unclear. This project sought to establish mechanistic links between trace metal availability and biogeochemical transformations in subsurface systems. Integrated field and laboratory studies of trace metal availability and biogeochemical processes were conducted in riparian wetlands in the Tims Branch watershed at the Savannah River Site, marsh wetlands at Argonne National Laboratory, and the streambed of East Fork Poplar Creek at Oak Ridge National Laboratory, with supplemental work with wetland soils from sites in Missouri and Florida.

54 ENVIRONMENTAL SCIENCES↗