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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A Computational Workflow of Elucidating Viral Impact on Mediating Microbial Response to In-situ Experimental Warming: Bridging microbial modeling to carbon and mineral modeling

Viruses are abundant in soils and shape microbial communities in ways that can potentially influence ecosystem processes, yet their contributions to carbon cycling and mineral transformations remain poorly understood. Here we present a multi-phase framework that links virus-host interactions to soil biogeochemistry by combining ecological simulations, genome- and community-scale metabolic modeling, and statistical and machine-learning analyses. We first calibrated microbial abundance profiles under explicit infection scenarios to capture how viral pressure alters community structure, then explored alternative interaction strategies, including kill-the-winner, piggyback-the-winner, and mixed lytic-lysogenic modes, through forward simulations. These ecological shifts were translated into metabolic consequences using exchange fluxes summarized into biologically meaningful categories, while integrated statistical and machine-learning screens elevated subtle but consistent signals. Application of this framework revealed that viral infections shift the balance between organic and inorganic fluxes, redirecting metabolism from diffuse organic transformations toward inorganic pools such as protons and CO 2 , directly linking viral regulation to respiration and soil carbon balance. The roll-up analysis also isolated perturbations in critical mineral ions, including magnesium, manganese, zinc, and copper, which serve as essential enzymatic cofactors. In piggyback-the-winner scenarios, uptake of these ions was strongly suppressed. Contrasting viral strategies produced distinct community structures and metabolic outcomes, from broad suppression under kill-the-winner dynamics to dramatic redistributions under high-lytic and high-gain lysogenic regimes that collapsed vulnerable microbial populations while promoting opportunists. Together, these results provide a tractable path to trace viral perturbations from host abundance shifts to metabolic flux adjustments and ecosystem-scale processes, offering a practical way to include viruses in earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Positive correlations between soil C stabilization and loss are regulated by roots, minerals, and microbes

Modern conceptual models of soil organic carbon (SOC) cycling place a strong focus on the microbe-mineral interactions that regulate C stabilization. However, the formation of ‘stable’ soil organic matter, which consists mainly of microbial residues bonded to mineral surfaces, is inextricably linked to C loss through microbial respiration. Therefore, what is the net impact of microbial metabolism on the total quantity of C held in the soil? To address this question, we constructed artificial root-soil systems to identify controls on C cycling across the plant-microbe-mineral continuum, simultaneously quantifying the formation of persistent mineral-associated C and C losses to respiration. Roots and minerals interacted to regulate these processes: while roots stimulated respiratory C losses and depleted mineral-associated C pools in low-activity clays, roots triggered formation of stable C in high-activity clays. Moreover, we observed a strong positive correlation between the formation of mineral-associated C and respiration. This suggests that the growth of persistent C pools which can resist subsequent disturbance comes at the expense of C loss from the system.

58 GEOSCIENCES↗
NASA NTRS2004

The Net Carbon Flux due to Deforestation and Forest Re-Growth in the Brazilian Amazon: Analysis using a Process-Based Model

We developed a process-based model of forest growth, carbon cycling, and land cover dynamics named CARLUC (for CARbon and Land Use Change) to estimate the size of terrestrial carbon pools in terra firme (non-flooded) forests across the Brazilian Legal Amazon and the net flux of carbon resulting from forest disturbance and forest recovery from disturbance. Our goal in building the model was to construct a relatively simple ecosystem model that would respond to soil and climatic heterogeneity that allows us to study of the impact of Amazonian deforestation, selective logging, and accidental fire on the global carbon cycle. This paper focuses on the net flux caused by deforestation and forest re-growth over the period from 1970-1998. We calculate that the net flux to the atmosphere during this period reached a maximum of approx. 0.35 PgC/yr (1PgC = 1 x 10(exp I5) gC) in 1990, with a cumulative release of approx. 7 PgC from 1970- 1998. The net flux is higher than predicted by an earlier study by a total of 1 PgC over the period 1989-1 998 mainly because CARLUC predicts relatively high mature forest carbon storage compared to the datasets used in the earlier study. Incorporating the dynamics of litter and soil carbon pools into the model increases the cumulative net flux by approx. 1 PgC from 1970-1998, while different assumptions about land cover dynamics only caused small changes. The uncertainty of the net flux, calculated with a Monte-Carlo approach, is roughly 35% of the mean value (1 SD).

Hirsch, A. I.↗
NASA NTRS2015

Variability of Phenology and Fluxes of Water and Carbon with Observed and Simulated Soil Moisture in the Ent Terrestrial Biosphere Model (Ent TBM Version 1.0.1.0.0)

The Ent Terrestrial Biosphere Model (Ent TBM) is a mixed-canopy dynamic global vegetation model developed specifically for coupling with land surface hydrology and general circulation models (GCMs). This study describes the leaf phenology submodel implemented in the Ent TBM version 1.0.1.0.0 coupled to the carbon allocation scheme of the Ecosystem Demography (ED) model. The phenology submodel adopts a combination of responses to temperature (growing degree days and frost hardening), soil moisture (linearity of stress with relative saturation) and radiation (light length). Growth of leaves, sapwood, fine roots, stem wood and coarse roots is updated on a daily basis. We evaluate the performance in reproducing observed leaf seasonal growth as well as water and carbon fluxes for four plant functional types at five Fluxnet sites, with both observed and prognostic hydrology, and observed and prognostic seasonal leaf area index. The phenology submodel is able to capture the timing and magnitude of leaf-out and senescence for temperate broadleaf deciduous forest (Harvard Forest and Morgan- Monroe State Forest, US), C3 annual grassland (Vaira Ranch, US) and California oak savanna (Tonzi Ranch, US). For evergreen needleleaf forest (Hyytiäla, Finland), the phenology submodel captures the effect of frost hardening of photosynthetic capacity on seasonal fluxes and leaf area. We address the importance of customizing parameter sets of vegetation soil moisture stress response to the particular land surface hydrology scheme. We identify model deficiencies that reveal important dynamics and parameter needs.

Soil moisture↗
DOE OSTI2020

Measured and Simulated Carbon Dynamics in Midwestern U.S. Corn‐Soybean Rotations

Abstract Corn ( Zea mays L.) and soybean ( Glycine max [L.] Merr.) production dominate Midwestern U.S. agriculture and impact the regional carbon and nitrogen cycles. Sustaining soil carbon is important for corn‐soybean production (CS); however, quantifying soil carbon changes requires long‐term field measurements and/or model simulations. In this study, changes in soil organic (SOC), inorganic (SIC), and total (TC) carbon; pH; total nitrogen (TN); and net ecosystem production (NEP) were measured in a conventional corn‐soybean rotation in central Iowa. Soil samples ( n = 42; 0–120 cm depth) were collected from two adjacent fields in 2005 and 2016. Eddy‐flux stations set up in the fields continuously monitored NEP from 2005–2016, and net biome production (NBP) was calculated using yield records. The DayCENT model was used to simulate the effects of conventional management practices on soil carbon and calibrated with field‐measured NEP and SOC. Measured soil TC (0–120 cm) decreased by −14.19 ± 6.25 Mg ha −1 , with highest reductions in SOC and SIC ( p < 0.05) at 0–15 and 90–120 cm, respectively. Measured TN decreased by −0.7 ± 0.29 Mg ha −1 with N‐accumulation at 60–90 cm ( p < 0.05). Eddy‐flux NBP decreased by −13.19 ± 0.05 Mg ha −1 . Soil and eddy‐flux records show a carbon reduction by −1.14 ± 0.63 and −1.20 ± 0.06 Mg ha −1 yr −1 , respectively. The validated DayCENT model suggests that all SOC pools declined. We postulate that conventional CS production has adverse effects on C and N dynamics in Midwestern United States.

Dold, C.↗
DOE OSTI2025

AquaMEND: Reconciling multiple impacts of salinization on soil carbon biogeochemistry

Soil salinization, exacerbated by climate change, poses a global threat to coastal ecosystem function and soil quality. Salinity influences carbon cycling through direct effects on microbial activity and indirect alterations to soil physicochemical properties including cation exchange, pH, and soil organic carbon availability. Current models inadequately represent these complexities, relying on linear reduction functions that overlook specific physicochemical changes induced by salinity. To address this gap, we propose an integrated model framework, AquaMEND, that combines microbial-explicit carbon decomposition and geochemical models. This model allows cation exchange and surface complexation processes to capture solute chemistry and nutrient availability in soils upon saltwater intrusion. Using response functions that capture salinity impacts on both salt-sensitive and salt-resistant microbial processes, AquaMEND simulates how the abiotic and biotic mechanisms work individually and collectively to regulate organic and inorganic pools and fluxes. Here, the parallel structure of aqueous and non-aqueous phases, together with microbial functions, result in a versatile model for solving dynamic coupling of organics, minerals and microbes under various environmental settings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Emerging multiscale insights on microbial carbon use efficiency in the land carbon cycle

Microbial carbon use efficiency (CUE) affects the fate and storage of carbon in terrestrial ecosystems, but its global importance remains uncertain. Accurately modeling and predicting CUE on a global scale is challenging due to inconsistencies in measurement techniques and the complex interactions of climatic, edaphic, and biological factors across scales. The link between microbial CUE and soil organic carbon relies on the stabilization of microbial necromass within soil aggregates or its association with minerals, necessitating an integration of microbial and stabilization processes in modeling approaches. In this perspective, we propose a comprehensive framework that integrates diverse data sources, ranging from genomic information to traditional soil carbon assessments, to refine carbon cycle models by incorporating variations in CUE, thereby enhancing our understanding of the microbial contribution to carbon cycling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

BEPAM Model Code and CABBI Simulation Results for "Assessing the Additional Carbon Savings with Biofuel"

This dataset consists of various input data that are used in the GAMS model. All the data are in the format of .inc which can be read within GAMS or Notepad. Main data sources include: acreage data (acre), crop budget data ($/acre), crop yield data (e.g. bushel/acre), Soil carbon sequestration data (KgCO2/ha/yr). Model details can be found in the "Assessing the Additional Carbon Savings with Biofuel" and GAMS model package. ## File Description (1) GAMS Model.zip: This includes all the input files and scripts for running the model (2) Table*.csv: These files include the data from the tables in the manuscript (3) Figure2_3_4.csv: This contains the data used to create the figures in the manuscript (4) BaselineResults.csv: This includes a summary of the model results. (5) SensitivityResults_*.csv: Model results from the various sensitivity analyses performed (6) LUC_emission.csv: land use change emissions by crop reporting district for changes of pasturelands to annual crops.

Anticipated baseline approach↗
DOE OSTI2022

How do soil microbes shape ecosystem biogeochemistry in the context of global change?

Earth system models disagree on the future of global soil carbon C, with projections ranging from losses of 70 Pg to gains of 250 Pg by the year 2100 (Todd-Brown et al., 2014). This disagreement is due, in part, to the high degree of uncertainty in the mechanisms that control soil C, the largest dynamic pool of organic C on Earth. It remains unclear how climate change, rising atmospheric CO2 levels, and other environmental changes will combine to affect global soil C. As key engineers of biogeochemical cycling, microbes play a crucial role in soil C responses to these environmental changes. Yet, the path toward representing microbes in soil models remains uncertain. Furthermore, we address four burning questions relevant for modelling microbial ecological, evolutionary, and biogeochemical processes in soils: (1) What is the role of soil microbes in biogeochemical cycling? (2) Does microbial community composition matter for soil carbon cycling? (3) Which ecological and evolutionary processes contribute to functional changes? (4) How should we model microbial eco-evolutionary mechanisms in soil C models?

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Near-Surface Hydrology and Soil Properties Drive Heterogeneity in Permafrost Distribution, Vegetation Dynamics, and Carbon Cycling in a Sub-Arctic Watershed: Modeling Archive

This Modeling Archive is in support of a NGEE-Arctic publication: Shirley et al. (2022) “Near-Surface Hydrology and Soil Properties Drive Heterogeneity in Permafrost Distribution, Vegetation Dynamics, and Carbon Cycling in a Sub-Arctic Watershed". [DOI].The dataset contains outputs from the global sensitivity analysis (GSA) of the “ecosys” model as reported in Shirley et al. (2022). The study showed that discontinuous permafrost environments are characterized by complex feedback loops and strong spatial heterogeneity which is created by variability in near-surface hydrology and soil properties. Additionally, the study demonstrated that missing representation of sub-grid heterogeneity in terrestrial ecosystem models can lead to biased estimates of the high-latitude carbon budget. Included in this dataset are the factor values for each run in the GSA and the model outputs used in this study. Included are two *.csv data files and one *.pdf.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

The age distribution of global soil carbon inferred from radiocarbon measurements

Soils contain more carbon than the atmosphere and vegetation combined. An increased flow of carbon from the atmosphere into soil pools could help mitigate anthropogenic emissions of carbon dioxide and climate change. Yet we do not know how quickly soils might respond because the age distribution of soil carbon is uncertain. Here we used 789 radiocarbon (Δ 14 C) profiles, along with other geospatial information, to create globally gridded datasets of mineral soil Δ 14 C and mean age. We found that soil depth is a primary driver of Δ 14 C, whereas climate (for example, mean annual temperature) is a major control on the spatial pattern of Δ 14 C in surface soil. Integrated to a depth of 1m, global soil carbon has a mean age of 4,830 ± 1,730 yr, with older carbon in deeper layers and permafrost regions. In contrast, vertically resolved land models simulate Δ 14 C values that imply younger carbon ages and a more rapid carbon turnover. Overall, our data-derived estimates of older mean soil carbon age suggest that soils will accumulate less carbon than predicted by current Earth system models over the twenty-first century. Reconciling these models with the global distribution of soil radiocarbon will require a better representation of the mechanisms that control carbon persistence in soils.

58 GEOSCIENCES↗
DOE OSTI2021

Soil carbon sequestration potential and the identification of hotspots in the Eastern Corn Belt of the United States

Soil carbon sequestration is a significant CO 2 mitigation strategy but precise assessments of sequestration require spatially explicit modeling of potential changes in soil organic carbon (SOC) in response to soil, climate, land condition and management interactions. We assessed the SOC sequestration potential of the Eastern Corn Belt (ECB) in the USA (Indiana, Kentucky, Maryland, Michigan, Ohio, Pennsylvania, and West Virginia) in response to the adoption of conservation farming practices and land use change (pasture and forestation) using the SOCRATES model. Input data was provided through an intersection of the STATSGO, National Land Cover Database and a PRISM climate surface. At the end of the 20th century, the 15.3 Mha of cropped soils in the ECB contained 632 Tg C, an estimated reduction of 52% since the introduction of agriculture in the mid-1800s. Complete adoption of no-tillage practices on Prime Cropland would potentially recover 147 Tg SOC over 20 years, whereas a continuation of conventional tillage would produce a loss of 35 Tg SOC. Sequestration hotspots (> 500 Gg increase in SOC) under no-tillage cover 2.3 Mha providing 28 Tg C over 20 years. The conversion of Marginal (non-Prime) agricultural lands to Forests would yield an additional 13 Tg C in SOC and 381 Tg C in aboveground biomass. The rehabilitation of Minelands to Forest would yield an additional 4 Tg C in SOC and 42 Tg C in biomass. Here, opportunities to sequester C in the ECB via tillage and reforestation are substantial and should be incorporated into regional and national climate change mitigation strategies.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2016

Soil Moisture Active Passive Mission L4_C Data Product Assessment (Version 2 Validated Release)

The SMAP satellite was successfully launched January 31st 2015, and began acquiring Earth observation data following in-orbit sensor calibration. Global data products derived from the SMAP L-band microwave measurements include Level 1 calibrated and geolocated radiometric brightness temperatures, Level 23 surface soil moisture and freezethaw geophysical retrievals mapped to a fixed Earth grid, and model enhanced Level 4 data products for surface to root zone soil moisture and terrestrial carbon (CO2) fluxes. The post-launch SMAP mission CalVal Phase had two primary objectives for each science product team: 1) calibrate, verify, and improve the performance of the science algorithms, and 2) validate accuracies of the science data products as specified in the L1 science requirements. This report provides analysis and assessment of the SMAP Level 4 Carbon (L4_C) product pertaining to the validated release. The L4_C validated product release effectively replaces an earlier L4_C beta-product release (Kimball et al. 2015). The validated release described in this report incorporates a longer data record and benefits from algorithm and CalVal refinements acquired during the SMAP post-launch CalVal intensive period. The SMAP L4_C algorithms utilize a terrestrial carbon flux model informed by SMAP soil moisture inputs along with optical remote sensing (e.g. MODIS) vegetation indices and other ancillary biophysical data to estimate global daily net ecosystem CO2 exchange (NEE) and component carbon fluxes for vegetation gross primary production (GPP) and ecosystem respiration (Reco). Other L4_C product elements include surface (10 cm depth) soil organic carbon (SOC) stocks and associated environmental constraints to these processes, including soil moisture and landscape freeze/thaw (FT) controls on GPP and respiration (Kimball et al. 2012). The L4_C product encapsulates SMAP carbon cycle science objectives by: 1) providing a direct link between terrestrial carbon fluxes and underlying FT and soil moisture constraints to these processes, 2) documenting primary connections between terrestrial water, energy and carbon cycles, and 3) improving understanding of terrestrial carbon sink activity in northern ecosystems. There are no L1 science requirements for the L4_C product; however self-imposed requirements have been established focusing on NEE as the primary product field for validation, and on demonstrating L4_C accuracy and success in meeting product science requirements (Jackson et al. 2012). The other L4_C product fields also have strong utility for carbon science applications; however, analysis of these other fields is considered secondary relative to primary validation activities focusing on NEE. The L4_C targeted accuracy requirements are to meet or exceed a mean unbiased accuracy (ubRMSE) for NEE of 1.6 g C/sq m/d or 30 g C/sq m/yr, emphasizing northern (45N) boreal and arctic ecosystems; this is similar to the estimated accuracy level of in situ tower eddy covariance measurement-based observations (Baldocchi 2008).

Cal/Val↗
DOE OSTI2020

Deeper snow increases the net soil organic carbon accrual rate in moist acidic tussock tundra: 210Pb evidence from Arctic Alaska

The net change in the carbon inventory of arctic tundra remains uncertain as global warming leads to shifts in arctic water and carbon cycles. To better understand the response of arctic tundra carbon to changes in winter precipitation amount, we investigated soil depth profiles of carbon concentration and radionuclide activities ( 7 Be, 137 Cs, 210 Pb, and 241 Am) in the active layer of a twenty-two-year winter snow depth manipulation experiment in moist acidic tussock tundra at Toolik Lake, Alaska. Depth correlations of cumulative carbon dry mass (g cm -2 ) vs. unsupported 210 Pb activity (mBq g -1 ) were examined using a modified constant rate of supply (CRS) model. Results were best fit by two-slope CRS models indicating an apparent step temporal increase in the accumulation rate of soil organic carbon. Most of the best-fit model chronologies indicated that the increase in carbon accumulation rate apparently began and persisted after snow fence construction in 1994. The inhomogeneous nature of permafrost soils and their relatively low net carbon accumulation rates make it challenging to establish robust chronologic records. Nonetheless, the data obtained in this study support a decadal-scale increase in net soil organic carbon accumulation rate in the active layer of arctic moist acidic tussock tundra under conditions of increased winter precipitation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Data for Zheng et al. (2025), "AquaMEND: Reconciling multiple impacts of salinization on soil carbon biogeochemistry"

Soil salinization, exacerbated by climate change, poses a global threat to coastal ecosystems and soil function. Salinity affects soil carbon cycling by directly impacting microbial activity and indirectly altering soil physicochemical properties, but current models inadequately represent these complexities. This dataset contains the observational and modeling data from Zheng et al. (2025), which described a process-based modeling framework that couples soil solution chemistry with microbial carbon cycling reactions to study the impacts of soil salinization. This conceptual model is implemented numerically into the open-source geochemical program PHREEQC 3.0 (Parkhurst and Appelo, 2013). This dataset consists of: - Figure2_AquaMEND_salinity_buffer: Contains model simulation outputs to assess the impact of three different cation exchange and surface complexation processes on salinity buffering (Fig. 2 from Zheng et al. 2025). - Figure3_Salinity_function: Contains salinity function fitting for literature data (Fig. 3 from Zheng et al. 2025). - Figure4_AquaMEND_microbial_mechanisms: Contains model simulation outputs for testing various microbial process-based hypotheses related to soil salinization, including microbial mortality, carbon use efficiency (CUE), extracellular enzyme activity, and other microbial mechanisms (Fig. 4 from Zheng et al. 2025). - Figure5_AquaMEND_Redox: Contains on model simulation outputs to evaluate shifts among key redox processes, such as aerobic respiration, sulfate reduction, and methanogenesis (Fig.5 from Zheng et al. 2025). - Figure6_AquaMEND_sorption: Contains on model simulation outputs for investigating the effects of salinity on dissolved organic matter (DOM) sorption and desorption processes (Fig. 6 from Zheng et al. 2025). - Figure7_AquaMEND_process_couple: Contains on model simulation outputs for exploring coupled biotic-abiotic processes and their interactions (Fig. 7 from Zheng et al. 2025). - data: Includes datasets used to develop salinity response functions and evaluate salinity buffering capacity. Datasets for MEND model calibration. - database: Contains the `.dat` file required by PHREEQC for model execution. - README.md: A Markdown plain text file describing the computational tools and directories. Files are a mixture of plain text CSV (comma-separated value) and plain text *.dat files written by the model; no special software is required to read them.

EARTH SCIENCE > AGRICULTURE > SOILS > SOIL SALINIT↗
DOE OSTI2022

Carbon acquisition ecological strategies to connect soil microbial biodiversity and carbon cycling

Soil carbon feedbacks to global change are uncertain, and the biological processes that govern soil organic matter decomposition are not resolved in current ecosystem models. Though it is recognized that microbial biodiversity influences decomposition rates, incorporating this relationship into ecosystem models is challenging because microbial communities are prohibitively diverse. It is likely necessary to distill microbial biodiversity by focusing on functional groups or ecological strategies. The ecological strategies that currently dominate the microbial ecology literature derive from macroecological theory, have clear weaknesses, and have had limited success when applied to predict soil carbon dynamics. Here, we present a new framework for soil microorganisms: Carbon Acquisition Ecological Strategies (CAES), and we outline a path toward incorporating microbial biodiversity into ecosystem models using this framework to enhance predictions of soil carbon feedbacks to global change. Because a microorganism's diet is central to its ecological niche and likely to covary with other ecologically significant traits, we posit that carbon acquisition may serve as a tractable foundation for developing ecological strategies. Further, we describe four candidate ecological strategies for soil microorganisms: 1° decomposers that assimilate complex plant polymers, 2° decomposers that assimilate microbial necromass, passive consumers that assimilate dissolved organic carbon, and predatory microbes that assimilate live microbial biomass. These strategies are directly linked to soil carbon pools currently represented in ecosystem models and may provide a foundation for greater integration of microbial community dynamics into ecosystem models.

59 BASIC BIOLOGICAL SCIENCES↗