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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Substrate-explicit Modeling Tutorial

This tutorial Narrative demonstrates how to apply thermodynamic theory, also known as lambda theory, to convert molecular formulas of compounds (derived from FTICR-MS peaks using Formulatiry and R codes) into stoichiometric and kinetic forms of biogeochemical reactions and how to use the resulting kinetic equations to simulate dynamic conversion of compounds in batch and continuous stirred tank reactors. It will address under what conditions respiration rates are driven by thermodynamics, and how respiration rates respond to the variations in parameters and input variables and how to interpret the results.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Iodate Reduction by Shewanella oneidensis Requires Genes Encoding an Extracellular Dimethylsulfoxide Reductase

Microbial iodate (IO 3 – ) reduction is a major component of the iodine biogeochemical reaction network in anaerobic marine basins and radioactive iodine-contaminated subsurface environments. Alternative iodine remediation technologies include microbial reduction of IO 3 – to iodide (I – ) and microbial methylation of I – to volatile gases. The metal reduction pathway is required for anaerobic IO 3 – respiration by the gammaproteobacterium Shewanella oneidensis . However, the terminal IO 3 – reductase and additional enzymes involved in the S. oneidensis IO 3 – electron transport chain have not yet been identified. In this study, gene deletion mutants deficient in four extracellular electron conduits (EECs; Δ mtrA , Δ mtrA -Δ mtrDEF , Δ mtrA -Δ dmsEF , Δ mtr A-ΔSO4360) and DMSO reductase (Δ dmsB ) of S. oneidensis were constructed and examined for anaerobic IO 3 – reduction activity with either 20 mM lactate or formate as an electron donor. IO 3 – reduction rate experiments were conducted under anaerobic conditions in defined minimal medium amended with 250 μM IO 3 – as anaerobic electron acceptor. Only the Δ mtrA mutant displayed a severe deficiency in IO 3 – reduction activity with lactate as the electron donor, which suggested that the EEC-associated decaheme cytochrome was required for lactate-dependent IO 3 – reduction. The Δ mtrA -Δ dmsEF triple mutant displayed a severe deficiency in IO 3 – reduction activity with formate as the electron donor, whereas Δ mtrA -Δ mtrDEF and Δ mtr A-ΔSO4360 retained moderate IO 3 – reduction activity, which suggested that the EEC-associated dimethylsulfoxide (DMSO) reductase membrane-spanning protein DmsE, but not MtrA, was required for formate-dependent IO 3 – reduction. Furthermore, gene deletion mutant Δ dmsB (deficient in the extracellular terminal DMSO reductase protein DmsB) and wild-type cells grown with tungsten replacing molybdenum (a required co-factor for DmsA catalytic activity) in defined growth medium were unable to reduce IO 3 – with either lactate or formate as the electron donor, which indicated that the DmsAB complex functions as an extracellular IO 3 – terminal reductase for both electron donors. Results of this study provide complementary genetic and phenotypic evidence that the extracellular DMSO reductase complex DmsAB of S. oneidensis displays broad substrate specificity and reduces IO 3 – as an alternate terminal electron acceptor.

, Shewanella oneidensis↗
DOE OSTI2024

Advancing a Watershed Hydro-Biogeochemical Theory: Linking Water Travel Time and Reaction Rates Under Changing Climate

The major goal of the project is to answer the question how and to what degree does a warming climate alter hydrological functioning and (biogeochemical and chemical weathering) reaction rates at the watershed scale? In particular, how does hydrological functioning (water storage, flow paths, and travel time) change responding to a warming climate? What are the corresponding alterations in biogeochemical and chemical weathering rates at the watershed scale? What is the general watershed-scale reaction rate law that causally links reaction rates to metrics of hydrological functioning that are determined by external hydroclimatic conditions and internal watershed structure characteristics? To answer these questions, we have used field measurements and reactive transport modeling. We have found that: 1) stream chemistry has altered tremendously in warmer years; 2) In this water-limited environment, hydrology is the dominant driver for soil respiration and carbon lateral export at the watershed scale; 3) deeper carbon respiration plays an essential role in regulating the patterns of stream carbon in low and high flow conditions, and deeper groundwater will become increasingly important as warming intensifies. This indicates in mountain streams, a warming climate will modify not only the timing and magnitude of streamflow as expected, but also the chemistry and quality of stream water.

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 OSTI2024

X-ray chemical imaging for assessing redox microsites within soils and sediments

Redox reactions underlie several biogeochemical processes and are typically spatiotemporally heterogeneous in soils and sediments. However, redox heterogeneity has yet to be incorporated into mainstream conceptualizations and modeling of soil biogeochemistry. Anoxic microsites, a defining feature of soil redox heterogeneity, are non-majority oxygen depleted zones in otherwise oxic environments. Neglecting to account for anoxic microsites can generate major uncertainties in quantitative assessments of greenhouse gas emissions, C sequestration, as well as nutrient and contaminant cycling at the ecosystem to global scales. However, only a few studies have observed/characterized anoxic microsites in undisturbed soils, primarily, because soil is opaque and microsites require µm-cm scale resolution over cm-m scales. Consequently, our current understanding of microsite characteristics does not support model parameterization. To resolve this knowledge gap, we demonstrate through this proof-of-concept study that X-ray fluorescence (XRF) 2D mapping can reliably detect, quantify, and provide basic redox characterization of anoxic microsites using solid phase “forensic” evidence. First, we tested and developed a systematic data processing approach to eliminate false positive redox microsites, i.e., artefacts, detected from synchrotron-based multiple-energy XRF 2D mapping of Fe (as a proxy of redox-sensitive elements) in Fe-“rich” sediment cores with artificially injected microsites. Then, spatial distribution of Fe II and Fe III species from full, natural soil core slices (over cm-m lengths/widths) were mapped at 1–100 µm resolution. These investigations revealed direct evidence of anoxic microsites in predominantly oxic soils such as from an oak savanna and toeslope soil of a mountainous watershed, where anaerobicity would typically not be expected. We also revealed preferential spatial distribution of redox microsites inside aggregates from oak savanna soils. We anticipate that this approach will advance our understanding of soil biogeochemistry and help resolve “anomalous” occurrences of reduced products in nominally oxic soils.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Sinuosity‐Driven Hyporheic Exchange: Hydrodynamics and Biogeochemical Potentials

Abstract Hydrologic exchange processes are critical for ecosystem services along river corridors. Meandering contributes to this exchange by driving channel water, solutes, and energy through the surrounding alluvium, a process called sinuosity‐driven hyporheic exchange. This exchange is embedded within and modulated by the regional groundwater flow (RGF), which compresses the hyporheic zone and potentially diminishes its overall impact. Quantifying the role of sinuosity‐driven hyporheic exchange at the reach‐to‐watershed scale requires a mechanistic understanding of the interplay between drivers (meander planform) and modulators (RGF) and its implications for biogeochemical transformations. Here, we use a 2D, vertically integrated numerical model for flow, transport, and reaction to analyze sinuosity‐driven hyporheic exchange systematically. Using this model, we propose a dimensionless framework to explore the role of meander planform and RGF in hydrodynamics and how they constrain nitrogen cycling. Our results highlight the importance of meander topology for water flow and age. We demonstrate how the meander neck induces a shielding effect that protects the hyporheic zone against RGF, imposing a physical constraint on biogeochemical transformations. Furthermore, we explore the conditions when a meander acts as a net nitrogen source or sink. This transition in the net biogeochemical potential is described by a handful of dimensionless physical and biogeochemical parameters that can be measured or constrained from literature and remote sensing. This work provides a new physically based model that quantifies sinuosity‐driven hyporheic exchange and biogeochemical reactions, a critical step toward their representation in water quality models and the design and assessment of river restoration strategies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Toward more mechanistic representations of biogeochemical processes in river networks: Implementation and demonstration of a multiscale model

A recently introduced multiscale model for representing the effects of small-scale hyporheic-zone biogeochemical processes is extended from the reach scale to river network scales. The model uses advection-dispersion-reaction equations for the channel network and one-dimensional advection-reaction subgrid models for the hyporheic zone. We summarize implementation in the integrated surface/subsurface hydrology modeling system Amanzi-ATS. The extension uses topologically defined meshes to represent stream/river networks and associates a hyporheic subgrid model with each channel grid cell. Biogeochemical reaction modeling capability residing in community software is accessed through an application programming interface. The implementation is verified against independent numerical solutions on a single reach. Mesh convergence studies show that commonly used semi-distributed representations can introduce significant spatial discretization error. Denitrification of farm runoff in a subbasin of the Portage River Basin in Ohio, USA is used to demonstrate the general-purpose reactive transport capability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

BioRT-Flux-PIHM v1.0: a biogeochemical reactive transport model at the watershed scale

Watersheds are the fundamental Earth surface functioning units that connect the land to aquatic systems. Many watershed-scale models represent hydrological processes but not biogeochemical reactive transport processes. This has limited our capability to understand and predict solute export, water chemistry and quality, and Earth system response to changing climate and anthropogenic conditions. Here we present a recently developed BioRT-Flux-PIHM (BioRT hereafter) v1.0, a watershed-scale biogeochemical reactive transport model. The model augments the previously developed RT-Flux-PIHM that integrates land-surface interactions, surface hydrology, and abiotic geochemical reactions. It enables the simulation of (1) shallow and deep-water partitioning to represent surface runoff, shallow soil water, and deeper groundwater and of (2) biotic processes including plant uptake, soil respiration, and nutrient transformation. The reactive transport part of the code has been verified against the widely used reactive transport code CrunchTope. BioRT-Flux-PIHM v1.0 has recently been applied in multiple watersheds under diverse climate, vegetation, and geological conditions. This paper briefly introduces the governing equations and model structure with a focus on new aspects of the model. It also showcases one hydrology example that simulates shallow and deep-water interactions and two biogeochemical examples relevant to nitrate and dissolved organic carbon (DOC). These examples are illustrated in two simulation modes of complexity. One is the spatially lumped mode (i.e., two land cells connected by one river segment) that focuses on processes and average behavior of a watershed. Another is the spatially distributed mode (i.e., hundreds of cells) that includes details of topography, land cover, and soil properties. Whereas the spatially lumped mode represents averaged properties and processes and temporal variations, the spatially distributed mode can be used to understand the impacts of spatial structure and identify hot spots of biogeochemical reactions. The model can be used to mechanistically understand coupled hydrological and biogeochemical processes under gradients of climate, vegetation, geology, and land use conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean

Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO 2 , NO, methanethiol, and methylamines were most abundant in the upwelling region. Here, we identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

MR13A-3183: Microbial and Geochemical Characterization of Groundwater: Implications for Underground Hydrogen Storage Leakage

Underground hydrogen storage (UHS) in geological formations is a key element of the clean energy transition as it enables the decarbonization of the transportation and industrial sectors by decoupling hydrogen production and storage. UHS has many benefits, including low cost, much wider availability, large storage capacity, well-established infrastructure, and increased safety because of geological sealing capabilities. However, the impact of hydrogen (H2) biogeochemical interactions in the presence of subsurface microorganisms is largely neglected from UHS perspectives. These interactions might affect the effectiveness of storage and can even cause H2 to leak into the shallow aquifers. Leakage of H2 into groundwater can change the geochemistry and induce several microbial-driven processes. Microorganisms, such as sulfate-reducers, are naturally abundant in groundwater and consume H2 to produce hydrogen sulfide (H2S), which can contaminate the freshwater drinking groundwater and cause damage to infrastructure. Hydrogen leakage can also trigger microbial reactions responsible for metal mobility, which can impact the water quality. However, the kinetics of these reactions and the temporal impact of hydrogen leakage in groundwater are still unknown. Therefore, a time series hydrogen-groundwater interaction experiment was conducted, and the changes in fluid chemistry and headspace gas composition will be analyzed along with DNA sequencing results to understand the extent and kinetics of biogeochemical reactions that occur if hydrogen leaks into groundwater. In the experiments, Ultra High Purity (UHP) hydrogen gas will be injected into glass vials with groundwater samples, for a designated time period. For each glass-sealed vial, 16S rRNA gene sequencing, IC, ICP-MS, and GC-TCD will be performed. The experiments provide insights into plausible impacts of hydrogen leakage into shallow drinking water aquifers.

Clark, Allison [West Virginia University (WVU)]↗
DOE OSTI2022

A perspective on iron (Fe) in the atmosphere: air quality, climate, and the ocean

As scientists engage in research motivated by climate change and the impacts of pollution on air, water, and human health, we increasingly recognize the need for the scientific community to improve communication and knowledge exchange across disciplines to address pressing and outstanding research questions holistically. Our professional paths have crossed because our research activities focus on the chemical reactivity of Fe-containing minerals in air and water, and at the air-sea interface. (Photo)chemical reactions driven by Fe can take place at the surface of the particles/droplets or within the condensed phase. The extent and rates of these reactions are influenced by water content and biogeochemical activity ubiquitous in these systems. One of these reactions is the production of reactive oxygen species (ROS) that cause damage to respiratory organs. Another is that the reactivity of Fe and organics in aerosol particles alter surficial physicochemical properties that impact aerosol-radiation and aerosol–cloud interactions. Also, upon deposition, aerosol particles influence ocean biogeochemical processes because micronutrients such as Fe or toxic elements such as copper become bioavailable. We provide a perspective on these topics and future research directions on the reactivity of Fe in atmospheric aerosol systems, from sources to short- and long-term impacts at the sinks with emphasis on needs to enhance the predictive power of atmospheric and ocean models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The PFLOTRAN Reaction Sandbox

Abstract. As modern reactive transport simulators evolve to accommodate the demands of a user community, researchers need a platform for prototyping new biogeochemical processes, many of which are niche and specific to laboratory or field experiments. The PFLOTRAN Reaction Sandbox leverages modern, object-oriented Fortran in an attempt to provide such an environment within an existing reactive transport simulator. This work describes the PFLOTRAN Reaction Sandbox concept and implementation through several illustrative examples. Reaction Sandbox Biodegradation Hill customizes the existing microbially mediated biodegradation reaction formulation within PFLOTRAN to better match empirical data. Reaction Sandbox Simple provides an isolated environment for testing numerous preconfigured kinetic rate expressions and developing user intuition. Reaction Sandbox Example serves as a template for creating new sandboxes within PFLOTRAN.

58 GEOSCIENCES↗
DOE OSTI2021

Impact of organic acids and sulfate on the biogeochemical properties of soil from urban subsurface environments

Urban subsurface environments are often different from undisturbed subsurface environments due to the impacts of human activities. For example, deterioration of underground infrastructure can introduce elevated levels of Ca, Fe, and heavy metals into subsurface soils and groundwater. Likewise, leakage from sewer systems can lead to contamination by organic C, N, S, and P. However, the impact of these organic and inorganic compounds on biogeochemical processes including microbial redox reactions, mineral transformations, and microbial community transitions in urban subsurface environments is poorly understood. Here we conducted a microcosm experiment with soil samples from an urban construction site to investigate the possible biotic and abiotic processes impacted when sulfate and acetate or lactate were introduced into an urban subsurface environment. In the top-layer soil (0-0.3 m) microcosms, which were highly alkaline (pH > 10), the major impact was on abiotic processes such as secondary mineral precipitation. In the mid-layer (2-3 m) soil microcosms, the rate of Fe(III)-reduction and the amount of Fe(II) produced were greatly impacted by the specific organic acid added, and sulfate-reduction was not observed until after Fe(III)-reduction was complete. Near the end of the incubation, some genera related to syntrophic acetate oxidation and methanogenesis were observed in the lactateamended microcosms. In the bottom-layer (7-8 m) soil microcosms, the rate of Fe(III)-reduction and the amount of Fe(II) produced were affected by the concentration of amended sulfate. Sulfate-reduction was concurrent with Fe(III)-reduction, suggesting that Fe(II) production was likely due to abiotic reduction of Fe(III) by sulfide produced by microbial sulfate reduction. The slightly acidic initial pH (~5.8) of the mid-soil system was a major factor controlling sequential microbial Fe(III) and sulfate reduction versus parallel Fe(III) and sulfate reduction in the bottom soil system, which had a neutral initial pH (~7.2). Finally, 16S rRNA gene-based community analysis revealed a variety of indigenous microbial groups including alkaliphiles, dissimilatory iron and sulfate reducers, syntrophes, and methanogens tightly coupled with, and impacted by, these complex abiotic and biogeochemical processes occurring in urban subsurface environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground

Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and 13 C enrichment in microorganisms, highlighting the potential to directly couple D 2 O or 13 C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Oxidation of Dissolved Tetravalent Selenium by Birnessite: Se Isotope Fractionation and the Effects of pH and Birnessite Structure

Redox reactions control the mobility and bioavailability of selenium (Se) in biogeochemical systems, both modern and ancient. Se isotope ratio measurements (e.g., 82 Se/ 76 Se) have been developed to enhance understanding of biogeochemical transformations and transport of Se. Stable isotope ratios of many elements are known to be powerful indicators of redox reactions, and shifts in 82 Se/ 76 Se have been observed for Se reduction reactions. However, Se isotope shifts caused by naturally relevant oxidation reactions have not been published. Here, we report Se isotope fractionation factors for oxidation of Se(IV) by birnessite. Experiments were conducted at pH = 4.0 and 5.5, with two types of birnessite of contrasting composition at two concentrations of suspended birnessite. The results are consistent with a single 82 Se/ 76 Se fractionation factor, for all times during all experiments, of 0.99767 (±0.0035 2 s.d.). Expressed as ε, the fractionation is 2.33‰ (±0.08‰).

58 GEOSCIENCES↗
DOE OSTI2021

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment

Iron reduction and sulfate reduction are two of the major biogeochemical processes that occur in anoxic sediments. Microbes that catalyze these reactions are therefore some of the most abundant organisms in the subsurface, and some of the most important. Due to the variety of mechanisms that microbes employ to derive energy from these reactions, including the use of soluble electron shuttles, the dynamics between iron- and sulfate-reducing populations under changing biogeochemical conditions still elude complete characterization. Here, we amended experimental bioreactors comprised of freshwater aquifer sediment with ferric iron, sulfate, acetate, and the model electron shuttle AQDS (9,10-anthraquinone-2,6-disulfonate) and monitored both the changing redox conditions as well as changes in the microbial community over time. The addition of the electron shuttle AQDS did increase the initial rate of Fe III reduction; however, it had little effect on the composition of the microbial community. Our results show that in both AQDS- and AQDS+ systems there was an initial dominance of organisms classified as Geobacter (a genus of dissimilatory Fe III -reducing bacteria), after which sequences classified as Desulfosporosinus (a genus of dissimilatory sulfate-reducing bacteria) came to dominate both experimental systems. Furthermore, most of the ferric iron reduction occurred under this later, ostensibly “sulfate-reducing” phase of the experiment. This calls into question the usefulness of classifying subsurface sediments by the dominant microbial process alone because of their interrelated biogeochemical consequences. To better inform models of microbially-catalyzed subsurface processes, such interactions must be more thoroughly understood under a broad range of conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Data from: “Significant stream chemistry response to temperature variations in a high-elevation mountain watershed”

High-elevation mountain regions, central to global freshwater supply, are experiencing more rapid warming than low-elevation locations. High-elevation streams are therefore potentially critical indicators for earth system and water chemistry response to warming. Here we present concerted hydroclimatic and biogeochemical data from Coal Creek, Colorado in the central Rocky Mountains at elevations of 2700 to 3700 m, where air temperatures have increased by about 2 °C since 1980. We analyzed water chemistry every other day from 2016 to 2019. Water chemistry data indicate distinct responses of different solutes to inter-annual hydroclimatic variations. Specifically, the concentrations of solutes from rock weathering are stable inter-annually. Solutes that are active in soils, including dissolved organic carbon, vary dramatically, with double to triple peak concentrations occurring during snowmelt and in warm years. We advocate for consistent and persistent monitoring of high elevation streams to record early glimpse of earth surface response to warming.1) Coal Creek stream were sampled and measured to answer the question if there is a significant stream chemistry response to climate change in high-elevation watershed2) The file contains data regarding discharge, water temperature and stream chemistry data for 2016-2019 year. Stream chemistry includes dissolved organic and inorganic carbon, chloride, nutrients, cations. The data collection efforts were carried out by the DOE-funded "Advancing a Watershed Hydro-Biogeochemical Theory: Linking Water Travel Time and Reaction Rates Under Changing Climate" project and Watershed Function SFA.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Data and Scripts associated with “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling.”

This data package is associated with the publication “Lambda-PFLOTRAN: Workflow for Incorporating Organic Matter Chemistry Informed by Ultra High Resolution Mass Spectrometry into Biogeochemical Modeling” submitted to Geoscientific Model Development (Muller et al., 2024). In this manuscript, organic matter chemistry and thermodynamics are directly connected to reactive transport simulators through the newly developed Lambda-PFLOTRAN (Parallel Reactive Flow and Transport model) workflow tool that succinctly incorporates organic matter chemistry data generated from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) into reaction networks to simulate aerobic respiration of the organic matter and the resulting biogeochemistry. Lambda-PFLOTRAN is a python-based workflow, executed through a Jupyter Notebook interface, that digests raw FTICR-MS data, develops a representative reaction network based on substrate-explicit thermodynamic modeling (also termed lambda modeling due to its key thermodynamic parameter λ used therein), and completes a biogeochemical simulation with the open source, reactive flow, and transport code PFLOTRAN. This data package contains Jupyter Notebook based workflows for two test cases for running biogeochemical simulations of organic matter oxidation identified by FTICR-MS. It contains four primary folders (workflow, data, src, and analysis), a file-level metadata file (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_flmd.csv) that lists all the files contained in this data package with a short description of each, and a data dictionary (Muller_2024_Lambda_PFLOTRAN_Manuscript_Data_Package_dd.csv) file that describes the tabular column headers. The ‘workflow’ folder contains the Jupyter Notebook based workflows for running the lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘data’ folder contains the FTICR-MS data, initial conditions, and incubation data for test cases 1 and 2 in folders titled ‘WHONDRS’ and ‘Colloids’, respectively. The data folder also has a ‘Database’ folder containing a reaction network for bulk organic matter (assumed to be CH2O) and a general database for PFLOTRAN (hanford_rxn_network). The CH2O reaction network defines bulk organic matter oxidation. Biogeochemical simulations are completed for both the lambda binned organic matter and bulk organic matter reaction networks. The ‘hanford_rxn_network’ database includes information required for PFLTORAN simulations including ion size, molar mass, and charge of the aqueous species, gases, and minerals phases. The ‘src’ folder contains python source codes for performing lambda analysis, PFLOTRAN simulation, sensitivity analysis and parameter estimation. The ‘analysis’ folder contains outputs from the test cases 1 and 2 including lambda analysis, PFLOTRAN runs and the calibration results.

54 ENVIRONMENTAL SCIENCES↗