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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Soil Biogeochemistry

Depending upon type and pedogenic stage, soils are subject to biotic and abiotic interactions of complex nature depending on type, nature and specific properties. Soil biogeochemistry involves the study of elemental cycling as mediated by complex and inseparable interactions between the biotic (living) and abiotic (non-living) components of soils. Human activities have substantially altered biogeochemical cycling of several key elements including carbon, nitrogen, phosphorus, potassium, and other secondary and minor nutrients over the past few decades, which, in turn, had serious environmental consequences. The present chapter outlines the soil biogeochemical investigations conducted within Indian subcontinent in both natural ecosystems and managed agricultural systems and addresses the state-of-the-art in order to understand the undergoing biogeochemical reactions. Here, we sought to clarify complex interactions generally occurred during biogeochemical transformations of an element (or compound) of interest within the type-specific soil. Further, we emphasized the importance of advancing our understanding of feedback loops in soil biogeochemical processes as altered by anthropogenic perturbations in tropical and sub-tropical soils of India. Overall, this chapter is broadly focused on the nutrient cycling, which is followed by more specific topics like “soil microbiology,” “soil biodiversity,” and “soil biotechnology.”

Sihi, Debjani↗
DOE OSTI2022

Quantifying pH buffering capacity in acidic, organic-rich Arctic soils: Measurable proxies and implications for soil carbon degradation

Dynamic pH change promoted by biogeochemical reactions in Arctic tundra soils can be a major control on the production and release of CO 2 and CH 4 , which contribute to rising global temperatures. Large quantities of soil organic matter (SOM) in these soils are susceptible to microbial decomposition, leading to pH changes during permafrost thaw. Soil pH buffering capacity (β) modulates the extent of pH change but has not been thoroughly studied and represented in predictive ecosystem scale biogeochemical models in Arctic tundra soils. In this study, we generated titration curves for 21 acidic tundra soils from three Arctic sites across northern Alaska, United States of America. Geochemical and hydrological soil properties were evaluated, and correlations with β were developed. Strong correlations between β and both gravimetric water content (Θ g ) (R 2 = 0.847, p < 0.001) and soil water retention (SWR) (R 2 = 0.849, p = 0.001) indicate that the ability of soil to retain water could be associated with its buffering properties. Correlations between β and soil organic carbon (SOC) and cation exchange capacity (CEC) were also explored, and relationships to SWR are discussed. These correlations were then used with existing soil databases reporting SOC, CEC, and SWR to estimate β across Alaska soils. We further demonstrated the quantitative relationships between β and the simulated rates of biogeochemical reactions and show that lower β leads to higher soil pH and more CH 4 production. Overall, our study provides simple proxies for β in Arctic soils and highlights the importance and implications of representing soil buffering in predictive models, thereby enabling quantitative coupling between pH dynamics associated with biogeochemical reactions. Integrating β into predictive models of Arctic biogeochemical cycling may reduce model uncertainty and further our understanding of permafrost SOM degradation accelerated by warming.

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

Biogeochemistry simulations for the Salt Marsh Accretion Response to Temperature eXperiment (SMARTX)

Coastal ecosystems have been largely ignored in Earth system models but are important zones for carbon and nutrient processing. Interactions between water, microbes, soil, sediments, and vegetation are important for mechanistic representation of coastal processes and ecosystem function. To investigate the role of these feedbacks, we used a reactive transport model (PFLOTRAN) that has the capability to be connected to the Energy Exascale Earth System Model (E3SM). PFLOTRAN was used to incorporate redox reactions and track chemical species important for coastal ecosystems as well as define simple representations of vegetation dynamics. Our goal was to incorporate oxygen flux, salinity, pH, sulfur cycling, and methane production along with plant-mediated transport of gases and tidal flux. Using porewater profile and incubation data for model calibration and evaluation, we were able to create depth-resolved biogeochemical soil profiles for saltmarsh habitat and use this updated representation to simulate direct and indirect effects of elevated CO2 and temperature on subsurface biogeochemical cycling. We found that simply changing the partial pressure of CO2 or increasing temperature in the model did not fully reproduce observed changes in the porewater profile, but the inclusion of plant or microbial responses to CO2 and temperature manipulations was more accurate in representing porewater concentrations. This indicates the importance of characterizing tightly coupled vegetation-subsurface processes for developing predictive understanding and the need for measurement of plant-soil interactions on the same time scale to understand how hotspots or moments are generated.Included in this data package are PFLOTRAN input (PFLOTRAN input files and chemical database) files for simulating single column biogeochemistry, root, and tide interactions at the Global Change Research Wetland (Kirkpatrick Marsh; Edgewater, MD). The biogeochemical network includes soil organic matter decomposition, nitrogen, iron, and sulfur cycling, and methanogenesis. Reduced species can be oxidized and plant processes include oxygen and nutrient priming, methane release, and nutrient uptake.Inputs:TAI_database.dat - geochemical database for reactions, more information on database structure and variables can be found here https://www.pflotran.org/documentation/user_guide/cards/pages/geochemical_database.htmlswamp.in - input file for biogeochemical network in PFLOTRANswamp_eCO2.in - input file for biogeochemical network in PFLOTRAN with input gas partial pressures/concentrations adjusted for elevated CO2 treatmentsOutputs:swamp_obs_0.tec - hourly porewater concentrations from from multiple depths in the soil columnswamp_eCO2_obs_0.tec - hourly porewater concentrations from multiple depths in the soil column for elevated CO2 treatmentsPFLOTRAN code access: https://github.com/fmyuan/pflotran-elm-interface.git

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

BioGeoChemistry of Actinides (LLNL SFA OBER - SBR FY20 Program Management and Performance Report)

The focus of the BioGeoChemistry of Actinides SFA is to identify and quantify the biogeochemical processes and the underlying mechanisms that control actinide mobility in an effort to reliably predict and control the cycling and migration of actinides in the environment. The research approach includes: (1) Field Studies (Research Thrust 1) that capture actinide behavior on the timescale of decades and (2) Fundamental Laboratory Studies (Research Thrust 2) that isolate specific biogeochemical processes observed in the field. These research thrusts are underpinned by the unique capabilities and staff expertise at Lawrence Livermore National Laboratory (LLNL), allowing the BioGeoChemistry of Actinides SFA to advance our understanding of actinide migration behavior in the environment, and serve as an international resource for environmental radiochemistry research (Figure 1). Research Thrusts 1 and 2 are guided by broad central hypotheses: Thrust 1 Hypothesis: Biogeochemical processes occurring on the timescale of years to decades lead to greater actinide recalcitrance in sediments and limit their migration in surface and groundwater. Thrust 2 Hypothesis: Long-term biogeochemical processes include mineral and surface alteration, which leads to stabilization of actinide surface associations or incorporation into mineral precipitates. Our strategic goal is to use the knowledge gained from our Science Plan to advance our understanding of the behavior of actinides, providing DOE with the scientific basis for remediation and long-term stewardship of DOE’s legacy sites and, more broadly, increasing our understanding of transport phenomena in environmental systems sciences with a particular emphasis on environmentally relevant (long-term) timescales. Although our focus is on actinide biogeochemistry, the increased focus on biogeochemistry at unique Test Bed locations associated with this SFA is providing fundamental information on redox processes and associated microbiological processes that control the cycling of redox sensitive metals under dynamic and transient biogeochemical conditions.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
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 OSTI2022

BioGeoChemistry at Interfaces (LLNL SFA OBER FY22 Program Management and Performance Report)

The focus of the BioGeoChemistry at Interfaces SFA is to identify and quantify the biogeochemical processes and the underlying mechanisms that control actinide mobility in an effort to reliably predict and control the cycling and migration of actinides in the environment. The research approach includes: (1) Field Studies that capture actinide behavior on the timescale of decades (Research Thrust 1), and (2) Fundamental Laboratory Studies that isolate specific biogeochemical processes observed in the field (Research Thrust 2). These Research Thrusts are underpinned by the unique capabilities and staff expertise at Lawrence Livermore National Laboratory, allowing the BioGeoChemistry at Interfaces SFA to advance our understanding of actinide migration behavior in the environment, and serve as an resource for environmental radiochemistry research internationally. In the past year, our greater focus on transient redox gradients across stratified waters, sediment-water interfaces, and mineral-water interfaces extended our research beyond actinides to address processes controlling cycling of redox-sensitive metals more broadly. Nevertheless, Research Thrusts 1 and 2 are guided by the following broad central hypotheses that were developed during our last program review held at the end of FY18: Thrust 1 Hypothesis: Biogeochemical processes occurring on the timescale of years to decades lead to greater actinide recalcitrance in sediments and limits their migration in surface and groundwater. Thrust 2 Hypothesis: Long-term biogeochemical processes include mineral and surface alteration, which leads to stabilization of actinide surface associations or incorporation into mineral precipitates. Our strategic goal is to use the knowledge gained from our Science Plan to advance our understanding of the behavior of actinides and other radionuclides (e.g. Cs) and provide DOE with the scientific basis for remediation and long-term stewardship of DOE’s legacy sites. More broadly, we will enhance our understanding of transport phenomena in environmental systems sciences with a particular emphasis on environmentally relevant (long-term) timescales. While we retain our focus on actinide biogeochemistry, our increased focus on overall biogeochemical processes occurring at unique Test Bed locations associated with this SFA provides fundamental information on abiotic and biotic redox processes that control the cycling of redox sensitive metals under dynamic and transient conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

LLNL SFA OBER FY23 Program Management and Performance Report: BioGeoChemistry at Interfaces

The focus of the BioGeoChemistry at Interfaces SFA has been to identify and quantify the biogeochemical processes and the underlying mechanisms that control actinide mobility in an effort to reliably predict and control the cycling and migration of actinides in the environment. The research approach has included: (1) Field Studies that capture actinide behavior on the timescale of decades (Research Thrust 1), and (2) Fundamental Laboratory Studies that isolate specific biogeochemical processes observed in the field (Research Thrust 2). These Research Thrusts are underpinned by the unique capabilities and staff expertise at Lawrence Livermore National Laboratory, allowing the BioGeoChemistry at Interfaces SFA to advance our understanding of actinide migration behavior in the environment, and serve as a resource for environmental radiochemistry research internationally (Figure 1). In FY23, our SFA research focused on transient redox gradients across stratified waters, sediment-water interfaces, and mineral-water interfaces to address processes controlling cycling of redox-sensitive metals. Nevertheless, Research Thrusts 1 and 2 are guided by the following broad central hypotheses that were developed during our last program review held at the end of FY18: Thrust 1 Hypothesis: Biogeochemical processes occurring on the timescale of years to decades lead to greater actinide recalcitrance in sediments and limits their migration in surface and groundwater. Thrust 2 Hypothesis: Long-term biogeochemical processes include mineral and surface alteration, which leads to stabilization of actinide surface associations or incorporation into mineral precipitates. Our strategic goal is to use the knowledge gained from our Science Plan to advance our understanding of the behavior of actinides and other radionuclides (e.g. Cs) and provide DOE with the scientific basis for remediation and long-term stewardship of DOE’s legacy sites. More broadly, we are improving our understanding of transport phenomena in environmental systems sciences with a particular emphasis on environmentally relevant (long-term) timescales. While we retained some of our historical focus on actinide biogeochemistry this past fiscal year, biogeochemical processes occurring at unique Test Bed locations associated with this SFA provide fundamental information on abiotic and biotic redox processes that control the cycling of redox sensitive metals under dynamic and transient conditions. Furthermore, in collaboration with SFA teams at Argonne National Laboratory, our SFA has begun to transition away from the current research focus and develop a new research program in terrestrial wetland systems. The Terrestrial Wetland Function and Resilience SFA program plan will be delivered to the Environmental System Science (ESS) program within BER at the end of FY23.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Editorial: Hydrology, ecology, and nutrient biogeochemistry at the terrestrial-aquatic interface

Terrestrial-aquatic interfaces (TAI) play important roles in mediating the exchange of water and chemicals between land, surface and subsurface water systems, which is tightly coupled with biogeochemical transformations that influence water quality and ecosystem health (Harvey and Gooseff, 2015; Harvey et al., 2019). Understanding and predicting the interactions between the hydrologic, ecologic, and biogeochemical processes at those interfaces is crucial for the sustainable management of water resources and promotion of healthy ecosystems under different environmental stresses and disturbances, including climate change, human activities, and more frequent occurrence of extreme events. Both process-based and data-driven approaches have emerged to address critical challenges at TAIs as integral parts of the Earth system (e.g., Ward and Packman, 2019; Chen et al., 2021; Dwivedi et al., 2022). In this Research Topic, we sought research that advances the understanding of coupled hydrologic, ecologic, and biogeochemical processes along various TAIs from the summit to sea, e.g., river corridors and coastal TAI systems. We invited observational, experimental, theoretical, analytical, numerical, and data-driven research that aims to understand hydro-biogeochemical processes such as the redox dynamics and biogeochemical transformations of carbon, nutrients, and metals occurring at the TAIs and address their heterogeneity and scaling challenges.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2023

The Sensitivity of the Equatorial Pacific ODZ to Particulate Organic Matter Remineralization in A Climate Model Under Pre-Industrial Conditions

Marine oxygen plays a fundamental role in regulating the transfer of organic carbon and nutrients to their dissolved inorganic forms, serving as the terminal electron acceptor for heterotrophic respiration. Oxygen can become limiting to these processes in coastal and open-ocean oxygen deficient zones (ODZs). The maintenance of ODZs depends on the balance between physical processes such as ventilation and biogeochemical processes such as remineralization. These two processes act in opposing directions on ODZs, with ventilation responsible for transporting oxygen from the surface, where it is near saturation with the partial pressure of O2 in the atmosphere, to deeper oxygen-depleted layers, and remineralization acting to consume oxygen through biogeochemical processes such as microbial degradation throughout the water column. Remineralization is represented in all CMIP6 models, but the actual parameterizations, as well as their magnitude, are widely varying. In this study, we examine the sensitivity to remineralization of the equatorial Pacific ODZ O2 ol/kg) in a model; the NASA GISS Ocean Biogeochemical Model (NOBM-G) embedded in the NASA-GISS coupled atmosphere-ocean model. We find that increasing the remineralization rate shoals the ODZ onset depth (i.e. the regionally averaged upper bound of the ODZ), and decreases ODZ volume and regional-averaged thickness. Changes in biological consumption and vertical convergence of oxygen are identified as the primary contributors to changes in ODZ onset depth. ODZ thickness is mainly influenced by the shoaling of the bottom boundary of the ODZ, which decreases with maximum remineralization rate due to decreasing oxygen consumption and increasing horizontal oxygen convergence in deep waters. On the other hand, vertically-averaged ODZ area has a more complex, non-monotonic relationship with maximum remineralization rate. While these findings suggest an important role for remineralization in determining the shape of the ODZ in our model, the relative importance of remineralization vs. other physical parameterizations remains to be established. While our results reflect the structure of our ocean biogeochemical model, the relationship of remineralization to ODZ characteristics in other models should be examined to better inform model inter-comparisons.

Oxygen-deficient zone↗
DOE OSTI2022

Tidal frequencies and quasiperiodic subsurface water level variations dominate redox dynamics in a salt marsh system

Salt marshes are hotspots of nutrient processing en route to sensitive coastal environments. Whilst our understanding of these systems has improved over the years, we still have limited knowledge of the spatiotemporal variability of critical biogeochemical drivers within salt marshes. Sea-level rise will continue to force change on salt marsh functioning, highlighting the urgency of filling this knowledge gap. Our study was conducted in a central California estuary experiencing extensive marsh drowning and relative sea-level rise, making it a model system for such an investigation. Here we instrumented three marsh positions subjected to different degrees of tidal inundation (6.7%, 8.9%, and 11.2% of the time for the upper, middle, and lower marsh positions, respectively), providing locations with varied biogeochemical characteristics and hydrological interactions at the site. We continuously monitored redox potential (Eh) at depths of 0.1, 0.3, and 0.5 m, subsurface water levels (WL), and temperature at 0.7 m depth at each marsh position. To understand how drivers of subsurface biogeochemical processes fluctuate across tidal cycles, we used wavelet analyses to explain the interactions between Eh and WL. We found that tidal forcing significantly affects key drivers of biogeochemical processes by imparting controls on Eh variability, likely driving subsurface hydro-biogeochemistry of the salt marsh. Wavelet coherence showed that the Eh-WL relationship is nonlinear, and their lead–lag relationship is variable. We found that precipitation events perturb Eh at depth over timescales of hours, even though WL shows relatively minimal change during events. Furthermore, this work highlights the importance of high frequency in situ measurements, such as Eh, to help explain factors that govern subsurface biogeochemistry and hydrological processes in salt marshes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Temporal Patterns in Soil Redox Potential Vary Across a Freshwater Coastal Delta

Widespread and persistent flooding is submerging coastal ecosystems, particularly along the Louisiana Gulf coast, where flooding results from the compounding effects of ground subsidence and rising sea level. Restoration projects aim to mitigate land loss by diverting sediment loads from rivers into degraded areas to increase ground elevation. To predict how coastal ecosystems will change over time in response to projected changes in relative sea level and restoration, it is necessary to understand how subsurface biogeochemical processes respond to dynamic hydrologic forcings. Here, this study evaluates how environmental parameters that integrate biogeochemical processes vary with water table fluctuations in the freshwater Wax Lake Delta (WLD) in Louisiana, USA, where water diversions have formed one of the only active deltas along the coast. High‐frequency observations of water level, soil redox potential, specific conductance and pH were made for 1 year along elevation transects located on the older, proximal and younger, distal ends of a deltaic island. Redox responded rapidly to changing water tables, with fluctuations occurring primarily in shallow soils (< 20 cm) and at higher elevations. Deeper soils and those at lower elevation remained inundated and reduced. Semi‐diurnal tidal fluctuations were pronounced in younger, distal soils, presumably due to rapid groundwater exchange with the river channel. Tidal signals were muted in older soils that instead exhibited seasonal variability associated with river discharge and evapotranspiration. Although much of the delta sediments are persistently reducing and anoxic, redox fluctuations in the natural levees that border the deltaic islands likely drive high rates of biogeochemical activity. Evaluating how hydrology drives the frequency and duration of redox fluctuations provides a basis for understanding how biogeochemical processes might vary with complex hydrological interactions in coastal systems.

Herndon, Elizabeth [Oak Ridge National Laboratory ↗
DOE OSTI2021

Effective kinetics driven by dynamic concentration gradients under coupled transport and reaction

Biogeochemical reaction kinetics are generally established from batch reactors where concentrations are uniform. In natural systems, many biogeochemical processes are characterized by spatially and temporally variable concentration gradients that often occur at scales which are not resolved by field measurements or biogeochemical and reactive transport models. Yet, it is not clear how these sub-scale chemical gradients affect reaction kinetics compared to batch kinetics. Here we investigate this question by studying the paradigmatic case of localized pulses of solute reacting with a solid or a dissolved species in excess. Additionally, we consider non-linear biogeochemical reactions, representative of mineral dissolution, adsorption and redox reactions, which we quantify using simplified power-law kinetics. The combined effect of diffusion and reaction leads to effective kinetics that differ quantitatively and qualitatively from the batch kinetics. Depending on the nonlinearity (reaction order) of the local kinetics, these effects lead to either enhancement or decrease of the overall reaction rate, and result in a rich variety of reaction dynamics. We derive analytical results for the effective kinetics, which are validated by comparison to direct numerical simulations for a broad range of Damköhler numbers and reaction order. Our findings provide new insights into the interpretation of imperfectly mixed lab experiments, the effective kinetics of field systems characterized by intermittent reactant release and the integration of sub-scale concentration gradients in reactive transport models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Quantifying the influence of different biocrust community states and their responses to warming temperatures on soil biogeochemistry in field and mesocosm studies

Biocrusts influence soil biogeochemistry by fixing carbon (C) and nitrogen (N) and through leachate inputs to soils. Functional rates can vary among biocrust community states and in response to edaphic properties, heterotrophic microbial activity, and global change. Using soils and biocrusts from the Colorado Plateau, Utah, USA, we aimed to quantify the influence of early-successional (ES) and late-successional (LS) biocrust community states on soil biogeochemistry. In a field setting, we found soil was less “fertile” under ES than LS biocrust, but ES biocrust had a relative influence 1.3 times greater than LS biocrust on soil fertility. Leachate collected from LS biocrust had, on average, 6 times more organic C and 1.7 times more dissolved N than ES biocrust, but concentrations of phosphorus (P) and inorganic N did not differ among the two biocrust types. Here, to disentangle influences of biocrusts and soil properties on biogeochemical pools, we constructed mesocosms from homogenized soil and left the surface bare or covered with ES or LS biocrust, before assignment to ambient or warmed (+5 °C) temperature treatments for 3 months. Multivariate biogeochemical properties differed among cover types, yet all exhibited losses of P, N, and organic C and nearly half of the biogeochemical variables considered did not differ among cover types. Mesocosms with LS biocrust retained more dissolved N, supported 8 additional, significant correlations among biogeochemical pools of the biocrust and mineral soil layer on average, and lost fewer of these correlations under warming. Overall, while soils under LS biocrusts were more fertile (i.e., had higher nutrient concentrations) than under ES, we did not find evidence implicating leachate as the primary driver of this difference. Biocrust influences on soil fertility were greater when mineral soil nutrients were in lower concentrations, highlighting the value of even incipient biocrusts for dryland functioning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Uranium Attenuated by a Wetland 50 Years after Release into a Stream

: Wetlands have several important roles in the hydrological cycle, including maintaining water quality by removing surface and groundwater contaminants. Over time, the wetlands themselves can become contaminated, posing a secondary environmental threat. The objective of this study was to calculate the inventory of uranium (U) remaining in a wetland 50 years after the Fuel Fabrication Facility on the Savannah River Site located in South Carolina released 43.5 Mg of U into the nearby environment. Over 232 700 gamma spectra and their associated global positioning system (GPS) coordinates were collected and collated into a map of the contaminated land area. Five core samples were also collected that contained U concentrations as high as 14 099 mg/kg (background levels are about 2.7 mg/kg U). The contaminated area was 278 000 m2 , and it contained 36.2 Mg U, about 83% of the U released. About 80% of the U in the wetland was concentrated in a former beaver pond, a 73 000 m2 area (26% of the contaminated area). This contaminated wetland area was almost 2 km from the source, indicating that it comprised unique hydro-biogeochemical properties for immobilizing the released U. To the best of our knowledge, this is the first data-rich study to quantify the long-term effectiveness of a wetland to immobilize inorganic contaminants. Significant environmental changes to the system, such as those associated with hydrology, forest fires, or anthropogenic land use, may alter the complex hydro-biogeochemical interactions necessary for the long-term immobilization of the U.

Contaminant inventory↗
DOE OSTI2021

Validation of the Community Land Model Version 5 over the Contiguous United States (CONUS) using in situ and remote sensing data sets

The Community Land Model (CLM) is an effective tool to simulate the biophysical and biogeochemical processes and their interactions with the atmosphere. Although CLM Version 5 (CLM5) constitutes various updates in these processes, its performance in simulating energy, water and carbon cycles over the Contiguous United States (CONUS) at scales which land surface changes and hydrometeorological and hydroclimatological applications are more locally relevant is yet to be assessed. In this study, we conducted three simulations at 0.125? during 1979-2018 over the CONUS using different configurations of CLM, namely CLM5-biogeochemistry (CLM5BGC), CLM4.5BGC, and CLM5-satellite phenology (CLM5SP). We validated and compared their simulations against multiple remote-sensed and in-situ datasets. Overall, the parametric and structural updates (e.g., carbon cost for nitrogen uptake, variable soil thickness, dry surface layer) in CLM5 improve its ability in capturing terrestrial biogeochemical dynamics. The low evapotranspiration in CLM5BGC is associated with biases in simulating vegetation phenological characteristics rather than soil water limitations. The mismatch between CLM5BGC-simulated peak leaf area index and reference data can be attributed to CLM5BGC's inability in simulating phenology of trees and grasses. The differences between CLM-simulated irrigation and reference estimates can be attributed to differences between processes represented in models and in reality, and uncertainties in input and validation datasets. Evaluation against observations at small catchments suggest that hydrologic parameters needed to be calibrated to improve simulations of runoff, especially subsurface runoff. Additional efforts are needed to incorporate spatially-distributed plant phenology and physiology parameters and regional-specific agricultural management practices (e.g., planting, harvest).

Cheng, Yanyan↗
DOE OSTI2023

Matrix Approach to Accelerate Spin-Up of CLM5

Numerical models have been developed to investigate and understand responses of biogeochemical cycle to global changes. Steady state, when a system is in dynamic equilibrium, is generally required to initialize these model simulations. However, the spin-up process that is used to achieve steady state pose a great burden to computational resources, limiting the efficiency of global modeling analysis on biogeochemical cycles. This study introduces a new Semi-Analytical Spin-Up (SASU) to tackle this grand challenge. We applied SASU to Community Land Model version 5 and examined its computational efficiency and accuracy. At the Brazil site, SASU is computationally 7 times more efficient than (or saved up to 86% computational cost in comparison with) the traditional native dynamics (ND) spin-up to reach the same steady state. Globally, SASU is computationally 8 times more efficient than the accelerated decomposition spin-up and 50 times more efficient than ND. In summary, SASU achieves the highest computational efficiency for spin-up on site and globally in comparison with other spin-up methods. It is generalizable to wide biogeochemical models and thus makes computationally costly studies (e.g., parameter perturbation ensemble analysis and data assimilation) possible for a better understanding of biogeochemical cycle under climate change.

54 ENVIRONMENTAL SCIENCES↗