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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

WHONDRS River Corridor Sediment and Water Geochemistry and In Situ Sensor Data from Machine-Learning-Informed Sites across the Contiguous United States (v6)

This dataset supports a broader study examining hyporheic zone respiration rates to improve predictive models at a contiguous United States (CONUS) scale. The CONUS-Scale Model-Sample Study (CM) was designed following ICON (integrated, coordinated, open, and networked) principles to facilitate a model-experiment (ModEx) iteration approach, leveraging crowdsourced sampling across the CONUS. New machine learning models were created every month to guide sampling locations. Data from the resulting samples were used to test and rebuild the machine learning models for the next round of sampling guidance. Sampling began in April 2022 and ended in October 2023. In addition to the widely distributed CONUS sites, a more spatially focused sampling occurred in the Yakima River Basin, WA in summer 2022. Data from this more spatially intensive sampling occurred under the label “Second Spatial Study (SSS)” and were also included in the machine learning models. Other data types collected from SSS that were not part of CM were published in a separate data package (https://data.ess-dive.lbl.gov/view/doi:10.15485/1969566). This data package was originally published in February 2023. It was updated in June 2023 (v2; new and modified files); December 2023 (v3; new and modified files); June 2024 (v4; new and modified files); April 2024 (v5; new and modified files); and September 2025 (v6; modified files). See the change history section in the readme for more details. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of two folders of field photos and videos, one folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data and one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) international generic sample number (IGSN) mapping file; (6) field protocols; (7) a subfolder with sample data; and (8) a subfolder with sensor data. The sample data subfolder contains (1) surface water and sediment dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data and averages; (2) surface water and sediment total nitrogen data and averages; (3) surface water major cations and anions and averages; (4) sediment grain size data; (5) sediment iron (II) data and averages; (6) wet sediment mass, dry sediment mass, water mass, and wet sediment volume in incubation and sediment ICR vials; (7) sediment incubation respiration rate data and averages; (8) normalized respiration rate data and averages; (9) methods codes; (10) sediment specific surface area; (11) sediment percent carbon and nitrogen; (12) sediment gravimetric moisture and averages; (15) sediment X-ray diffraction (XRD) data; (16) sediment adenosine triphosphate (ATP) and averages; (17) a subfolder with sediment incubation respiration data, scripts, and plots; (18) surface water and sediment FTICR methods; and (19) a subfolder of 9.4 Tesla (9.4T) FTICR-MS data. This folder contains five subfolders, one containing the sediment .xml data files, one containing the water .xml files, one containing the sediment CoreMS output files, one containing the water CoreMS output files, and the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS).The sensor data subfolder contains (1) a subfolder with miniDOT dissolved oxygen and temperature data and plots; (2) miniDOT dissolved oxygen and temperature summary data; and (3) miniDOT installation methods. All files are .csv, .pdf, .R, .xml, .d, .html, .Rmd, .py, .cal, .json, .jpg, .jpeg, .png, .mov, or .mp4. CORRECTION: Carbon and nitrogen content are reported as percentages. The current column headers "01395_C_percent_per_mg" and "01397_N_percent_per_mg" are incorrect. These should read "01395_C_percent" and "01397_N_percent" and will be corrected in the next version of this data package. We thank the United States Forest Service, Washington Department of Fish and Wildlife, Washington Department of Natural Resources, Cowiche Canyon Conservatory, Washington State Parks and Recreation Commission (Scientific Research Permit #210901), and the Confederated Tribes and Bands of the Yakama Nation for access to field locations where the samples labeled “SSS” were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview. WHONDRS consortium members were asked to provide any acknowledgments for the collection of samples labeled “CM” and the following is a list of acknowledgments that were submitted with their corresponding Site IDs: (MART) Research activities were conducted in part on the Wind River Experimental Forest within the Gifford Pinchot National Forest; (MP- 100379) Philadelphia is part of Lenapehoking, the ancestral homelands of the Lenape peoples; (MP-102398) Land surveyed is the ancestral homelands of the Nookhose'iinenno (Arapaho), Tsis tsis'tas (Cheyenne), and Nuuchu (Ute); (MP-100749 and MP- 100747) Georgia Coastal Ecosystem LTER, OCE-1832178; (SP-70 and SP-72) Eastern Shoshone, Shoshone-Bannock; (MP- 102944) Funded by Oregon Watershed Enhancement Board. On the traditional lands of the Confederated Tribes of the Siletz, Confederated Tribes of the Grand Rhonde, and the Clatsop-Nehalem Confederated Tribe; (MP- 100607) Holiday Creek is located on the traditional territory of the Monacan Indian Nation; (SP-45) Lafayette Blue Springs State Park; (MP-102420) NSF DEB-2016749; (MP-100019) New Hampshire Agriculture Experiment Station; (SP-35) Rayonier (land owner; https://www.rayonier.com/); (MP- 101276) US Department of Energy, Office of Science, Biological and Environmental Research, Subsurface Biogeochemical Research, Watershed Dynamics and Evolution SFA at ORNL; (MP- 103224) Watershed Dynamics and Evolution SFA at ORNL; (MP- 101584) Traditional lands of the Oceti Sakowin (Dakota, Lakota, Nakoda) and Anishinaabe Peoples.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1991

Sulfate reduction in deep-sea sediments

Sulfate reduction rates calculated from about 200 DSDP pore water sulfate profiles have been contoured and plotted on a map covering most areas of the world ocean. Rates show a remarkable spatial consistency, with high rates observed near the continental margins, becoming progressively lower toward the central ocean basins. Relatively elevated rates are also found in the eastern equatorial Pacific, a site of upwelling and correspondingly high rates of primary organic production. Overall, the distribution of sulfate reduction in pelagic sediments looks very similar to the distribution of primary organic carbon production. When rates are directly compared, however, the correlation between sulfate reduction and primary production is only moderately strong. Perhaps the most important influence on sulfate reduction is sediment deposition rate and the control this has over the fraction of the sedimentary organic carbon flux that becomes available for sulfate reduction. The slower the rate of sediment deposition the more time for oxic respiration and the less organic carbon that escapes to the zone of sulfate reduction. To predict most accurately sulfate reduction rates, however, the variables of primary production, water depth, and sediment deposition rate must all be integrated.

NASA Program Exobiology↗
DOE OSTI2025

Pyrogenic Organic Matter Laboratory Experiment: Aerobic Respiration and Geochemistry from Variably Inundated Stream Sediments (v3)

This dataset supports a broader study examining the effects of variable inundation and pyrogenic organic matter on ecosystem respiration. The dataset provides data generated from a laboratory batch experiment investigating the interaction between variable inundation conditions (wet and dry sediment) and pyrogenic organic matter (burned and unburned treatments). The contents include time series dissolved oxygen, sediment geochemistry data, and field metadata (including qualitative information on instream and river corridor characteristics). This data package was originally published in November 2025. It was updated in April 2026 (v2; new and modified files) and May 2026 (v3; modified files). See the change history section in the readme for more details For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) international generic sample number (IGSN) mapping file; (5) readme; (6) field protocol; (7) sample name metadata; (8) an environmental context picture for the dry and inundated sampling locations; and (9) a subfolder with sample data from the sediment incubation experiment. The sample data subfolder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC); (2) total nitrogen (TN); (3) gravimetric moisture; (4) partial pressure and production rates of carbon dioxide, methane, and nitrous oxide; (5) field wet sediment mass, dry sediment mass, water mass, and field wet sediment volume in incubation and sediment NPOC/TN vials; (6) methods codes; (7) respiration rates, pH, and temperature from after the incubation, raw time series dissolved oxygen and temperature, and a subfolder containing associated plots and scripts; (8) ions; (9) FTICR-MS methods; and (10) a subfolder of 12 Tesla (12T) FTICR-MS data. This folder contains the CoreMS processed data and three subfolders, one containing the .xml files, one containing the CoreMS output files, and the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .xml, .html, .Rmd, .py, .cal, .json, or .jpg.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Integration of Omics into a New Comprehensive Rate Law for Competitive Terminal Electron-Accepting Processes in Reactive Transport Models: Application to N, Fe, S, and Contaminant Transformations in Stream and Wetland Sediments

Surface waters represent important sources of alternate energy and drinking water in the United States, and characterizing the biogeochemical processes that affect surface water quality is relevant to the DOE-BER mission. Sediment biogeochemical processes regulate the release of carbon (C), nutrients, and contaminants to surface waters and thus influence water quality. Sediment biogeochemical processes are dynamic and affected by the deposition and remobilization of solid material and changes in environmental conditions driven by water discharge variations. Wetlands are important natural filters of surface waters which may either trap, metabolize, or mobilize nutrients and contaminants. Despite their importance, biogeochemical processes regulating nutrient and contaminant release and C transformation in stream and wetland sediments cannot be predicted accurately by current mathematical models. These reactive transport models largely rely on detectable changes in geochemical conditions to activate metabolic processes, do not accurately account for the competition between microbial processes, and poorly constrain effects of hydrological perturbations on biogeochemical processes. In this BER-SBR exploratory project, metagenomic and geochemical signatures were combined to identify microbially-mediated redox processes in anaerobic stream and wetland sediments from the Savannah River Site (SRS, ANL SFA) and East Fork Poplar Creek (EFPC, ORNL SFA) that play important roles in C, uranium (U), and mercury (Hg) transformations. In addition, sediment incubations were conducted to examine the competition between anaerobic respiration processes Finally, new rate laws were developed for reactive transport models that rely on complementary metagenomic and geochemical signatures to identify the underlying anaerobic microbial processes in stream and wetland sediments, describe the competition between the dominant metabolic processes involved in nutrient release and U and Hg mobilization, and more accurately quantify carbon transformation and the response of microbial processes to changes in redox conditions associated with hydrological forcing. These rate laws were optimized in batch reactors with SRS wetland sediments, where iron and sulfate reduction dominate. Anaerobic carbon remineralization processes followed the expected thermodynamic sequence of microbial respiration with depth in both sediments, except that geochemical signals indicated that sulfate reduction was inactive in EFPC sediments and moderate in SRS wetland sediments. Estimates indicated that microbial iron reduction contributed to at least half of the production of reduced iron in these sediments. Incubations demonstrated that nitrate reduction, denitrification, and dissimilatory nitrate reduction to ammonium were active in the natural EFPC sediment and activated upon nitrate amendment in these nitrate-rich sediments. In turn, these processes were outcompeted by the addition of either iron oxides or sulfate as alternative terminal electron acceptors. Although geochemical products of sulfate reduction were not detected in the incubations, the abundance of sulfate reduction genes increased with depth in the sediment and was equally more pronounced in treatments amended with either iron oxides or sulfate. Simultaneously, anaerobic sulfide oxidizing bacteria coupling sulfide oxidation to DNRA (and not conventional denitrification) were apparently enriched over time, regardless of the treatments. These findings indicate that sulfate reduction is important in freshwater stream sediments and probably catalyzed by a cryptic sulfur cycle involving nitrogen species, in which the sulfur products from sulfate reduction are immediately removed by side reactions and not detectable by geochemical measurements alone. Similar experiments in SRS sediments, however, demonstrated little interaction between nitrogen and sulfur cycling microorganisms. Sulfate reduction was impacted by the addition of more thermodynamically favorable electron acceptors, suggesting either that iron-reducing microorganisms outcompeted sulfate-reducing microorganisms for organic substrate, depleting the stock of electron donor available for sulfate reduction, or that the cryptic sulfur cycle was shunted by the precipitation of FeS generated as a result of the abiotic reduction of iron oxides by dissolved sulfide. A diagnostic modeling exercise was conducted to further investigate the competition between terminal electron accepting processes. As conventional kinetic models typically do not account for cryptic cycles and used inaccurate formulations to describe competition between microbial communities, new metabolic rate laws were developed that explicitly express the electron acceptor-specific enzyme of each energetically favorable metabolic process based on gene abundance detected in the incubations. The model was tested with the sediment slurry incubation data to determine whether substrate competition could explain the decrease in sulfate reduction observed in the presence of iron oxide competitor. The model was able to reproduce geochemical concentrations really well in each treatment once the model was calibrated with the unamended control, suggesting that microbial competition was indeed driven by thermodynamic considerations. Overall, carbon remineralization processes and rates will be reproduced much more realistically with the new metabolic rate laws.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Respiration data, microbial community assembly data, and FTICR-MS data associated with: “Disturbance Triggers Non-Linear Microbe-Environment Feedbacks. Sengupta et al., 2021, Biogeosciences”

This data package is associated with the manuscript “Disturbance Triggers Non-Linear Microbe-Environment Feedbacks, in revision in Biogeosciences (Sengupta et al. and 2021;https://bg.copernicus.org/preprints/bg-2021-51/). The study used hyporheic zone sediments as a model system to provide an integrated view of how disturbance modulates linkages among microbial ecology, biogeochemistry, and organic matter thermodynamics. Laboratory experiments exposed hyporheic sediment to varying wetting/drying dynamics. Data types include dissolved oxygen rates used to derive respiration rates, Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) data used to derive thermodynamic properties of organic matter, and microbial community assembly metrics derived from amplicon-sequence data of putatively active (cDNA) and whole community (gDNA). The outcomes of the study are condensed into a broadly applicable conceptual model linking external forcing, internal dynamics, and history. This data package is comprised of a file-level metadata (FLMD) csv, metadata csv, and seven folders that contain csv files, R scripts, xml files, and associated documentation: (1) Rates, (2) bNTI, and (3) FTICR, (4) Statistics_Analyses, (5) Raw OTU Beta dispersion Analysis, (6) bMNTD Randomizations, and (7) Data Dictionaries. The FLMD file has a description of each file included in the data package.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment

Abstract The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption—impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01–4.7 fmol SO42− cell−1 h−1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23–40 nmol h−1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.

Lindsay, Melody R.↗
DOE OSTI2026

Model scripts associated with “Revisiting controls on hyporheic respiration with knowledge-guided machine learning at continental scale”

NOTE: The manuscript associated with this data package is currently in review. The data/scripts may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final scripts and additional metadata. This data package is associated with the publication “Revisiting controls on hyporheic respiration with knowledge-guided machine learning at continental scale” submitted to Environmental Science & Technology (Zheng et al. 2026). The project combines mechanistic process modeling with knowledge-guided machine learning (KGML) to evaluate how organic matter chemistry, microbial biomass, and physical substrate accessibility regulate realized respiration rates across river corridors. All data used in this paper have been previously published and can be accessed at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1729719 (Goldman et al., 2020). This data package contains 3 R-markdown (Rmd) preprocessing scripts for the previously published data and subsequent modelling workflows. The full workflow with input and output data can be found in the associated GitHub repository at https://github.com/jianqiuz/KGML-WHONDRS.

Biogeochemistry↗
DOE OSTI2026

Point-scale organic-matter decomposition in streambeds is weakly associated with reach-scale respiration

Stream and river ecosystems play a central role in the movement and decomposition of particulate organic matter, serving as a conduit between terrestrial hillslopes and coastal environments. Microbial-catalyzed decomposition generates simpler organic molecules that fuel respiration, often in the sediments of these ecosystems. However, the degree of connection between sediment-associated respiration (ER??d) and organic-matter decomposition remains poorly understood. How that relationship compares to decomposition’s relationship with whole ecosystem (ERtot) and water column (ERwc) respiration is also not clear. We examined the link between particulate organic matter decomposition—using cellulose-based cotton strips as a standardized substrate—and all three components of respiration across 48 sites in the environmentally diverse Yakima River Basin (Washington State, USA). We hypothesized that decomposition within sediments would be most strongly related to ERsed, but decomposition rates were more closely associated with ERtot, with little connection to ERsed or ERwc. This suggests that particulate organic matter decomposition within stream/river sediments reflects integrated system respiration rather than processes confined to sediments or the water column alone. Further, across the basin, decomposition rates nearly spanned the previously reported global range for streams and rivers and were best explained by total dissolved nitrogen (TDN), sediment grain size, and aridity of the upstream drainage area. These results highlight the strong influence of land cover and basin-scale biophysical variation on sediment-associated decomposition processes and indicate that mechanistic models of organic matter decomposition in streams/rivers should account for coupled sediment–water–land interactions.

Stegen, James C. (ORCID:0000000191357424)↗
DOE OSTI2022

Transition Zone Morphology Dynamics of Dissolved Oxygen (DO) in a Salinity-Impacted Hyporheic Zone

Freshwater salinization is a common yet underappreciated environmental problem in rivers, yet how this process impacts the transport of dissolved oxygen (DO) in the hyporheic zone remains unknown. Here, using flume experiments and numerical simulations, we have demonstrated that the morphological dynamics of the DO transition zone are controlled by the dimensionless number Da·Ra –2 , a measure of the rate of aerobic respiration to free convection. At low Da·Ra –2 , the oxic front breaks up into fingers which subsequently grow, and leads to accelerating of DO transport and shrinking of the anaerobic zone in the underlying sediment. As Da·Ra –2 increases, the growth rate of the instability decreases, and the DO plume fingers are suppressed and delayed compared with the saltwater-freshwater interface, the mixing area between saltwater and freshwater. These results indicate that the freshwater salinization syndrome can have significant impacts on the functioning of aquifer ecosystems unless regulated and managed effectively.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1993

Pathways of organic carbon oxidation in three continental margin sediments

We have combined several different methodologies to quantify rates of organic carbon mineralization by the various electron acceptors in sediments from the coast of Denmark and Norway. Rates of NH4+ and Sigma CO2 liberation sediment incubations were used with O2 penetration depths to conclude that O2 respiration accounted for only between 3.6-17.4% of the total organic carbon oxidation. Dentrification was limited to a narrow zone just below the depth of O2 penetration, and was not a major carbon oxidation pathway. The processes of Fe reduction, Mn reduction and sulfate reduction dominated organic carbon mineralization, but their relative significance varied depending on the sediment. Where high concentrations of Mn-oxide were found (3-4 wt% Mn), only Mn reduction occurred. With lower Mn oxide concentrations more typical of coastal sediments, Fe reduction and sulfate reduction were most important and of a similar magnitude. Overall, most of the measured O2 flux into the sediment was used to oxidized reduced inorganic species and not organic carbon. We suspect that the importance of O2 respiration in many coastal sediments has been overestimated, whereas metal oxide reduction (both Fe and Mn reduction) has probably been well underestimated.

NASA Discipline Exobiology↗
DOE OSTI2025

Laboratory time series moisture manipulative experiment from sediment across San Antonio, Texas: time series aerobic respiration and geochemistry

This dataset supports a broader study examining the effects of wetting and drying on hyporheic zone respiration. The dataset provides data generated from a laboratory moisture manipulation experiment. The contents include time series aerobic respiration and moisture; dissolved oxygen; sediment geochemistry data; and field metadata (including qualitative information on instream and river corridor characteristics). Samples were collected as part of the WHONDRS Allison Veach collaboration (AV1). The data package associated with the AV1 study is available at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/2529428. AV1 sampling occurred across 7 perennial and 7 intermittent streams in San Antonio, Texas. Each stream/site was visited both in summer during base flow (July-September 2023) and winter during peak flow (January-February 2024). This study uses subsamples from a subset of AV1 samples. The original field samples were labeled as AV1_###. Subsequent subsamples for this study were labeled as EV_###. The labels from the field samples and the EV subsamples can be mapped directly based on the digits following the prefix and underscore (i.e., EV_001 is a subsample from AV1_001). See the critical details section below for more details on sample naming. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) field protocol; and a (6) a subfolder with sediment sample data from the incubation experiment. The sample data subfolder contains (1) effect size; (2) iron (II); (3) gravimetric moisture; (4) respiration rates; (5) raw dissolved oxygen values and plots; (6) specific conductance; (7) pH; (8) temperature; (9) a summary containing mean, median, and standard deviation values of each data type for each treatment (wet and dry); and (10) methods codes. All files are .csv or.pdf.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Laboratory time series moisture manipulative experiment from sediment across the contiguous US: time series aerobic respiration and geochemistry (v2)

This dataset supports a broader study examining the effects of wetting and drying on hyporheic zone respiration across the contiguous United States (CONUS). The dataset provides data generated from a laboratory moisture manipulation experiment. The contents include time series aerobic respiration and moisture; dissolved oxygen; sediment geochemistry data; and field metadata (including qualitative information on instream and river corridor characteristics). Samples were collected as part of the WHONDRS CONUS-Scale Model-Sample Study (CM). This study was designed following ICON (integrated, coordinated, open, and networked) principles to facilitate a model-experiment (ModEx) iteration approach, leveraging crowdsourced sampling across the CONUS. The data package associated with the CM study is available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1923689. CM sampling began in April 2022 and ended in October 2023. This study uses subsamples from a subset of CM samples collected between June 2022 and June 2023. The original field samples were labeled as CM_###. Subsequent subsamples for this study were labeled as EC_###. The labels from the field samples and the EC subsamples can be mapped directly based on the digits following the prefix and underscore (i.e., EC_001 is a subsample from CM_001). See the critical details section below for more details on sample naming. This data package was originally published in August 2024. It was updated in February 2026 (v2; new and modified files). See the change history section in the readme for more details. For details on how to navigate this data package, see this infographic from the River Corridor SFA https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data and one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) field protocol; and a (6) a subfolder with sediment sample data from the incubation experiment. The sample data subfolder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC); (2) total nitrogen (TN); (3) adenosine triphosphate (ATP); (4) percent carbon and nitrogen; (5) effect size; (6) iron (II); (7) gravimetric moisture; (8) respiration rates and raw dissolved oxygen values; (9) specific conductance; (10) pH; (11) temperature; (12) a summary containing median values of each data type for each treatment (wet and dry); (13) methods codes; (14) FTICR-MS methods; and (15) a subfolder of 9.4 Tesla FTICR-MS data. This folder contains three subfolders, one containing the sediment .xml data files, one containing the sediment CoreMS output files, the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .ref, or .xml.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1979

Microbial Sulfate Reduction Measured by an Automated Electrical Impedance Technique

Electrical impedance measurements are used to investigate the rates of sulfate reduction by pure cultures of and sediments containing sulfur-reducing bacteria. Changes in the electrical impedance ratios of pure cultures of Desulfovibrio aestuarii and samples of reduced sediments from San Francisco Bay were measured by a Bactometer 32, and sulfate reduction was followed by measuring the incorporation of (S-35) sulfate into metal sulfides. The growth of the bacteria in pure culture is found to result in an increase of 0.2200 in the impedance ratio within 24 h, accompanied by increases in protein, ATP, sulfide and absorptance at 660 nm, all of which are inhibited by the addition of molybdate. Similar responses were observed in the sediments, although impedance ratio responses were not completely inhibited upon the addition of molybdate, due to the presence of nonsulfate-respiring microorganisms. Experiments conducted with sterile media and autoclaved sediments indicate that the presence of H2S together with iron is responsible for the impedance effect, and sulfate reduction rates ranging between 0.85 and 1.78 mmol/l per day are estimated for the sediments by the impedance technique.

Oremland, R. S.↗
DOE OSTI2020

Microbially mediated iron redox cycling of subsurface sediments from Hanford Site, Washington State, USA

Iron-bearing clay minerals are predominant in soils and sediments, and they undergo oxidation-reduction cycles as a result of natural processes such as wetting/drying cycles and plant root respiration. However, the kinetics and mechanisms of multiple redox cycles of iron in clay-rich sediments and consequences of such cycling on sediment properties are poorly understood. The objective of this study was to understand how multiple redox cycles of Fe in clay-rich sediment affect the rate and extent of Fe bioreduction and the physicochemical properties of the sediment. A natural sediment sample containing Fe-bearing montmorillonite from Hanford, Washington, USA was size-fractionated [2.0 to 0.5 μm (Hanford-C) and 0.5 to 0.02 μm (Hanford-F)] and redox-cycled for four times. Bioreduction was achieved utilizing Geobacter sulfurreducens and re-oxidization was performed with sparged air. Time-course change of total Fe (II) was monitored to measure the rate and extent of Fe (III) bioreduction. Redox-cycled sediments were characterized to determine the physicochemical changes. Both the initial rate and extent of bioreduction fluctuated across the four redox cycles, but they ultimately decreased from 5.3 μmol g -1 h -1 and 22.9% to nearly zero by the fourth cycle. These fluctuation patterns were likely due to a combined effect of reductive dissolution of small/poorly crystalline clay particles (by 3–5%) and clay mineral structural changes, as evidenced by redox induced changes of aqueous chemistry, surface area, cation exchange capacity, mineralogy, and Mössbauer parameters. Once these small/poorly crystalline clay particles were dissolved, structural Fe in residual larger and more crystalline clay particles was largely reversible across additional redox cycles, as revealed by Mössbauer spectroscopy through the first three cycles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Continental-Scale Controls on Hyporheic Respiration Revealed by Knowledge-Guided Machine Learning

Hyporheic zone sediments regulate organic matter turnover and in-stream respiration, yet controls on sediment respiration remain poorly constrained across heterogeneous river networks, limiting prediction of stream metabolism and carbon processing at continental scales. Here, we integrate observations from ~90 river corridors across the United States in the WHONDRS consortium with a knowledge-guided machine learning (KGML) framework that couples thermodynamic rate theory with machine learning to identify dominant controls on hyporheic respiration. Diagnostic analyses show that organic matter concentration and thermodynamic favorability define an upper bound on respiration potential, whereas biological catalytic capacity and physical accessibility jointly govern realized respiration rates through interaction effects. To represent unmeasurable accessibility constraints, we use the mechanistic model as a scaffold for KGML, allowing machine learning to target residual structure not explained by process theory. This hybrid framework improves predictive skill relative to both the mechanistic model alone and fully data-driven models while preserving interpretability. These results indicate that variability in hyporheic respiration is largely mechanistically structured and demonstrate how integrating process theory with explainable AI enhances predictive performance while enabling scalable synthesis of river corridor observations.

Zheng, Jianqiu↗
DOE OSTI2021

Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea

Abstract Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100 µM increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Moisture-mineral interactions drive bacterial and organic matter turnover in glacier-sourced riparian sediments undergoing pedogenesis

Glacial recession is occurring at unprecedented rates resulting in increased sediment accumula-tions in some riverine ecosystems. Increased sediment deposition has implications for ecosystem stability (e.g., floods and river paths) and environmental services (e.g., carbon sequestration). Soils and sediments have an enormous potential to retain carbon (C), predominantly due to sorp-tion to mineral surfaces. However, C persistence may be sensitive to climate-change induced temperature and moisture variations. We coupled ultrahigh resolution organic matter composition classification with bacterial characterization and respiration measurements to test the combined effects of temperature (4 vs 20°C) and moisture (50 vs 100% water-filled pore space) on C turn-over in sediments maintained under different mineralogical conditions (illite-amended vs non-amended). Here we show that the inhibition of CO 2 emissions from the combined effect of in-creased moisture content and illite was reflected in the turnover of key molecular signatures, such as the nominal oxidation state of C, often irrespective of temperature. However, shifts in bacteri-al communities from a coupled moisture-mineral interaction, were temperature-dependent. Our results highlight the importance of moisture in driving mineral-organic interactions and suggest that C in clay-rich, water-saturated sediments is both thermodynamically unfavorable and miner-al-protected from microbial consumption.

58 GEOSCIENCES↗
DOE OSTI2025

Water Column Respiration in the Yakima River Basin is Explained by Temperature, Nutrients and Suspended Solids

Understanding aquatic ecosystem metabolism involves the study of two key processes: carbon fixation via primary production and organic C mineralization as total ecosystem respiration (ERtot). In streams and rivers, ERtot includes respiration in the water column (ERwc) and in the sediments (ERsed). While literature surveys suggest that ERsed is often a dominant contributor to ERtot, recent studies indicate that the relative influence of sediment-associated processes versus water column processes can fluctuate along the river continuum. Still, a comprehensive understanding of the factors contributing to these shifts within basins and across stream orders is needed. Here we contribute to this need by measuring ERwc and collecting water samples across 47 sites in the Yakima River basin, Washington, USA. We found that ERwc rates varied throughout the basin during baseflow conditions, ranging from –7.38 to 0.36 g O2 m?3 d?1, and encompassed the range of ERwc literature values. Additionally, by comparing to ERtot estimates for rivers across the contiguous United States, we suggest that the contribution of ERwc rates to reach-scale ERtot rates across the Yakima River was likely highly variable, but we did not test this directly. We observed that temperature, nutrient concentrations (dissolved organic carbon, total dissolved nitrogen), and total suspended solids explained 41% of ERwc variability across the basin. Our findings highlight the potential relevance of water column processes in aquatic ecosystem metabolism, with the Yakima River basin serving as an environmentally diverse river network representative of the larger Columbia River basin that spans much of the Pacific Northwest region of the United States. Our results are generally congruent with previous work, suggesting that the observed variability and suite of associated environmental factors influencing ERwc are potentially transferable across basins.

Laan, Maggi M.↗