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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana

Two bacterial strains, 1N T and 5N T , were isolated from hemlock forest soil using a soluble organic matter enrichment. Cells of 1N T (0.65×1.85 µm) and 5N T (0.6×1.85 µm) are Gram-stain-negative, aerobic, motile, non-sporulating and exist as single rods, diplobacilli or in chains of varying length. During growth in dilute media (≤0.1× tryptic soy broth; TSB), cells are primarily motile with flagella. At higher concentrations (≥0.3× TSB), cells of both strains increasingly form non-motile chains, and cells of 5N T elongate (0.57×~7 µm) and form especially long filaments. Optimum growth of 1N T and 5N T occurred at 25–30 °C, pH 6.5–7.0 and <0.5% salinity. Results of comparative chemotaxonomic, genomic and phylogenetic analyses revealed that 1N T and 5N T were distinct from one another and their closest related type strains: Paraburkholderia madseniana RP11 T , Paraburkholderia aspalathi LMG 27731 T and Paraburkholderia caffeinilytica CF1 T . The genomes of 1N T and 5N T had an average nucleotide identity (91.6 and 91.3%) and in silico DNA–DNA hybridization values (45.8%±2.6 and 45.5%±2.5) and differed in functional gene content from their closest related type strains. The composition of fatty acids and patterns of substrate use, including the catabolism of phenolic acids, also differentiated strains 1N T and 5N T from each other and their closest relatives. The only ubiquinone present in strains 1N T and 5N T was Q-8. The major cellular fatty acids were C 16 : 0 , 3OH-C 16 : 0 , C 17 : 0 cyclo, C 19 : 0 cyclo ω8 c and summed features 2 (3OH-C 14 : 0 / C 16 : 1 iso I), 3 (C 16 : 1 ω6 c /ω7 c ) and 8 (C 18 : 1 ω7 c /ω6 c ). A third bacterium, strain RL16-012-BIC-B, was isolated from soil associated with shallow roots and was determined to be a strain of P. madseniana (ANI, 98.8%; 16S rRNA gene similarity, 100%). Characterizations of strain RL16-012-BIC-B (DSM 110723=LMG 31706) led to proposed emendments to the species description of P. madseniana . Our polyphasic approach demonstrated that strains 1N T and 5N T represent novel species from the genus Paraburkholderia for which the names Paraburkholderia solitsugae sp. nov. (type strain 1N T =DSM 110721 T =LMG 31704 T ) and Paraburkholderia elongata sp. nov. (type strain 5N T =DSM 110722 T =LMG 31705 T ) are proposed.

Microbiology↗
DOE OSTI2021

SoDaH: the SOils DAta Harmonization database, an open-source synthesis of soil data from research networks, version 1.0

Data collected from research networks present opportunities to test theories and develop models about factors responsible for the long-term persistence and vulnerability of soil organic matter (SOM). Synthesizing datasets collected by different research networks presents opportunities to expand the ecological gradients and scientific breadth of information available for inquiry. Synthesizing these data is challenging, especially considering the legacy of soil data that have already been collected and an expansion of new network science initiatives. To facilitate this effort, here we present the SOils DAta Harmonization database (SoDaH; https://lter.github.io/som-website, last access: 22 December 2020), a flexible database designed to harmonize diverse SOM datasets from multiple research networks. SoDaH is built on several network science efforts in the United States, but the tools built for SoDaH aim to provide an open-access resource to facilitate synthesis of soil carbon data. Moreover, SoDaH allows for individual locations to contribute results from experimental manipulations, repeated measurements from long-term studies, and local- to regional-scale gradients across ecosystems or landscapes. Finally, we also provide data visualization and analysis tools that can be used to query and analyze the aggregated database. The SoDaH v1.0 dataset is archived and available at https://doi.org/10.6073/pasta/9733f6b6d2ffd12bf126dc36a763e0b4 (Wieder et al., 2020).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Soil temperature and soil moisture raw data, permafrost table depths, and accompanying environmental variable data, Kenai Wildlife Refuge, 2019-2022

Data package purpose: This data package was created to contain all data used in an upcoming article, "Canopy Cover and Microtopography Control Precipitation-Enhanced Thaw of Ecosystem-Protected Permafrost." In review.This data package includes: Raw output from 19 distributed temperature profilers with a thermistor every 10 cm along a 160 cm length at a measurement interval of 15 minutes (.CSV). Raw output from two soil moisture and temperature profilers (90 cm length and 120 cm length) that took composite soil moisture readings every 15 cm along the sensor length at a measurement interval of 30 minutes (.CSV). Permafrost depths were measured annually in mid-September at DTP sensor locations (.CSV) and along an across-site transect (.CSV). Environmental variables (snow depth, canopy closure, moss depth, and elevation) for all sensor locations. Real-time kinetic (RTK) GPS points showing site microtopography (.CSV).Analysis software: Our analysis was done in Matlab. File types can be used with any software.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Triple oxygen isotope compositions of globally distributed soil carbonates record widespread evaporation of soil waters

The stable isotopic composition of pedogenic carbonates is central to many studies of past climate and topography, providing a basis for our understanding of Earth's terrestrial history. A core assumption of many applications of oxygen isotope values (δ 18 O) of pedogenic carbonate is that they reflect the δ 18 O value of precipitation (rain/snow). Here, this assumption is violated if soil carbonates form in evaporated soil waters. In this work, we develop a means to identify evaporation in ancient soils using the triple oxygen isotope composition ( 16 O- 17 O- 18 O) of pedogenic carbonates.

58 GEOSCIENCES↗
DOE OSTI2022

A new bioenergy model that simulates the impacts of plant‐microbial interactions, soil carbon protection, and mechanistic tillage on soil carbon cycling

Abstract Advancing our predictive understanding of bioenergy systems is critical to design decision tools that can inform which feedstock to plant, where to plant it, and how to manage its production to provide both energy and ecosystem carbon (C) benefits. Here, we lay the foundation for that advancement by integrating recent developments in the science of belowground processes in shaping the C cycle into a new bioenergy model, FUN‐BioCROP (Fixation and Uptake of Nitrogen‐Bioenergy Carbon, Rhizosphere, Organisms, and Protection). We show that FUN‐BioCROP can approximate the historical trajectory of soil C dynamics as natural ecosystems were successively converted into intensive agriculture and bioenergy systems. This ability relies in part on a novel tillage representation that mechanistically models tillage as a process that increases microbial access to C. Importantly, the impacts of tillage and feedstock choice also influence FUN‐BioCROP simulations of warming responses with no‐till perennial feedstocks, miscanthus, and switchgrass, having more C that is unprotected and susceptible to warming than tilled annual feedstocks like corn–corn–soybean. However, this susceptibility to warming is balanced by a greater potential for increases in belowground C allocation to enhance soil C stocks in perennial systems. Collectively, our model results highlight the importance of belowground processes in evaluating the ecosystem C benefits of bioenergy production.

09 BIOMASS FUELS↗
DOE OSTI2026

A network of soil moisture, soil temperature, air temperature, net radiation, ground heat flux and ground water for Chicago, Illinois

This dataset contains environmental monitoring data collected using solar-powered Multi-Function Research (MFR) Long Range Wide Area (LoRaWAN)-enabled nodes at 11 sites in Chicago, Illinois, as part of the DOE Urban Integrated Field Lab CROCUS project. The MFR node system consists of an Input/Output Digital Input Module (IB8) interface box (ICT International) providing wired connections for environmental sensors and an MFR-Node-L data logger that manages power, data processing, and LoRaWAN communication. The wireless data are ingested via Sage network (https://sagecontinuum.org/) nodes that contain LoRaWAN antennae. Measurements were collected from 11 MFR nodes deployed across Chicago State University (CSU), Northeastern Illinois University (NEIU), Northwestern University (NU), University of Illinois Chicago (UIC), West Woodlawn "Blacks in Green" (BIG), and Indian Boundary Prairies (IBP). Each MFR node supports a consistent suite of sensors measuring atmospheric, soil, and hydrological variables. Atmospheric measurements include 2m air temperature (°C), 2m vapor pressure deficit (kPa), and 2m shortwave/longwave radiation (incoming and outgoing, W/m²) measured using ATH-VPD and Apogee SN500 sensors. Soil measurements include volumetric water content (VWC, %) and temperature (°C) at four depths (15, 30, 45, and 60 cm below surface) using Meter Teros54 sensors, and heat flux (W/m²) at 10 cm depth using Huske HFP01-05 sensors. At selected locations, Meter Hydros21 sensors measure groundwater depth (mm), specific conductivity (dS/m), and temperature (°C). The dataset includes timestamps, site identifiers with location names, device IDs, Global Positioning System (GPS) coordinates, variable names with units, measurement depths, values, sensor names, and Sage node identifiers. All timestamps are in local Chicago time (CDT/CST). Quality control flags are provided using a 6-bit binary system indicating physical range violations, step spikes, 24-hour flat-line conditions, 6-hour jitter, 7-day ultra-low variance, and persistent high offset. Data is provided in CSV and CF-compliant NetCDF formats. This dataset is part of a larger collection of CROCUS environmental monitoring data, including linked datasets from Air Quality Transmitter (AQT) sensors, Weather Transmitter (WXT) sensors, and Sap Flow Meter (SFM1x) sensors.

Chicago↗
DOE OSTI2024

Modeling the impact of measured and projected climate and management systems on agricultural fields: Surface runoff, soil moisture, and soil erosion

Abstract As global climate change poses a challenge to crop production, it is imperative to prioritize effective adaptation of agricultural systems based on a scientific understanding of likely impacts. In this study, we applied an integrated watershed modeling framework to examine the impacts of projected climate on runoff, soil moisture, and soil erosion under different management systems in Central Oklahoma. The proposed model uses measured climate data and three downscaled ensembles from the Coupled Model Intercomparison Project Phase 6 (CMIP6) at the water resources and erosion watershed to understand the impact of climate change and various climate conditions under three management systems: (1) continuous winter wheat (Triticum aestivum) under conventional tillage (WW‐CT; baseline system), (2) continuous winter wheat under no‐till (WW‐NT), and (3) cool and warm season forage cover crop mixes under no‐till (CC‐NT). The study indicates that the occurrence of agricultural drought is projected to increase while erosion rates will remain unchanged under the WW‐CT. In contrast, climate simulations imposed on the WW‐NT and CC‐NT systems significantly reduce runoff and sediment while preserving soil moisture levels. Especially, implementing the CC‐NT system can bolster food security and foster sustainable farming practices in Central Oklahoma in the face of a changing climate.

Environmental Sciences & Ecology↗
DOE OSTI2025

Imprint of Anthropogenic Sources and Soil Removal on the Surface Concentration of H2 in the Contiguous US

Hydrogen (H2) is experiencing renewed interest throughout the world as a low carbon fuel alternative or complement to fossil fuels. Significant uncertainties remain regarding the environmental impact of increasing H2 usage, in part due to gaps in our understanding of the H2 atmospheric budget, including the H2 release from industrial activities and the H2 soil removal, the most important sink of H2. This study focuses on H2 dry air mole fractions measured by the NOAA Global Monitoring Laboratory in discrete ambient air samples collected every few days at sites located in the contiguous United States between 2010 and 2022. We take advantage of the long-term observations from this network to study the regional distribution of H2 sources using the potential source contribution function (PSCF). We find that H2 PSCF is consistent with a large anthropogenic source of atmospheric H2 from the incomplete combustion of fossil fuel. However, episodic air masses with high H2 dry air mole fractions (>700 ppb) recorded at some sampling locations in the Western and Southeastern US are not associated with elevated CO, suggesting significant noncombustion anthropogenic or geological sources of H2. Air masses depleted in H2 are recorded in rural or remote continental sites. Our analysis of observations from a tall tower in NE Colorado suggests that the degree of H2 depletion not only reflects differences in soil exposure but also the regional inhibition of the soil sink under arid conditions.

Paulot, Fabien↗
DOE OSTI2023

A simple soil mass correction for a more accurate determination of soil carbon stock changes

Abstract Agricultural soils can act as a sink for large quantities of soil organic carbon (SOC) but can also be sources of carbon to the atmosphere. The international standard for assessing SOC stock and measuring stock change stipulates fixed depth sampling to at least 30 cm. The tendency of bulk density (BD) to decrease with decreasing disturbance and increasing SOC concentration and the assumption of constant SOC and BD within this depth profile promotes error in the estimates of SOC stock. A hypothetical but realistic change in BD from 1.5 to 1.1 g cm −3 from successive fixed depth sampling to 30 cm underestimates SOC stock change by 17%. Significant effort has been made to evaluate and reduce this fixed depth error by using the equivalent soil mass (ESM) approach, but with limited adoption. We evaluate the error in SOC stock assessment and change generated from fixed depth measurements over time relative to the ESM approach and propose a correction that can be readily adopted under current sampling and analytical methods. Our approach provides a more accurate estimate of SOC stock accumulation or loss that will help incentivize management practice changes that reduce the environmental impacts of agriculture and further legitimize the accounting practices used by the emerging carbon market and organizations that have pledged to reduce their supply chain greenhouse gas (GHG) footprints.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Workflow for Process Automation of Soil Gas Results from an Automated Soil Gas-Sampling System for Application in Carbon Storage Projects

Conference presentation at Geoconvention, Calgary, Alberta, Canada, May 12–14, 2025. The Energy & Environmental Research Center (EERC) developed an automated workflow for processing soil gas measurements collected from the automated soil gas-sampling systems deployed across the project site. Raw soil gas measurements are collected from each station every 4 hours and automatically uploaded to a cloud database. The workflow begins by writing code to download the data to a workstation automatically, then the data are published to an online dashboard that visualizes the measurements in time-series plots and a process-based decision-making framework. This automated workflow accelerates the time from data acquisition to decision-making. It supports carbon storage project operators by preparing and delivering a live, standardized dataset for quick analysis and source attribution to provide assurance of containment and overall permit compliance.

02 PETROLEUM↗
DOE OSTI2025

Workflow for Process Automation of Soil Gas Results from an Automated Soil Gas-Sampling System for Application in Carbon Storage Projects

Extended abstract for Geoconvention, Calgary, Alberta, Canada, May 12–14, 2025. The Energy & Environmental Research Center (EERC) developed an automated workflow for processing soil gas measurements collected from the automated soil gas-sampling systems deployed across the project site. Raw soil gas measurements are collected from each station every 4 hours and automatically uploaded to a cloud database. The workflow begins by writing code to download the data to a workstation automatically, then the data are published to an online dashboard that visualizes the measurements in time-series plots and a process-based decision-making framework. This automated workflow accelerates the time from data acquisition to decision-making. It supports carbon storage project operators by preparing and delivering a live, standardized dataset for quick analysis and source attribution to provide assurance of containment and overall permit compliance.

02 PETROLEUM↗
DOE OSTI2021

A reporting format for field measurements of soil respiration

Field observations of the soil-to-atmosphere CO2 flux–soil respiration, RS–are a prime example of ‘long tail’ data that historically have had neither centralized databases nor an agreed-upon reporting format. This has hindered scientific transparency, analytical reproducibility, and novel syntheses with respect to this globally-important component of the carbon cycle. Here we propose a new data and metadata reporting format for RS data, based on engagement with a wide range of researchers in the field as well as expert advisory panels. Our goal was a reporting format that would be relevant and useful for synthesis activities, and optimizing data discoverability and usability while not placing an undue burden on data contributors. We describe previous RS data collection efforts, lessons learned from related databases and data-oriented networks (e.g. FLUXNET) in earth and ecological sciences, and the process of community consultation. The proposed reporting format focuses on chamber-level data and metadata, specifying measurement conditions and, for a given measurement period defined by beginning and ending timestamps, a mean RS flux (or CO2 concentration) and associated ancillary measurements. Fundamentally, this format aims to enable findable, accessible, interoperable, and reusable data, while providing ‘future-proofing’ capabilities to support reanalyses using as yet unknown algorithms or approaches. Finally, this proposed RS reporting format is available online, and is intended to be a dynamic document, subject to further community feedback and/or change in the future.

Bond-Lamberty, Benjamin↗
DOE OSTI2023

Continuous soil temperature and soil deformation measurements, Teller road Mile 47, Nome, Alaska.

The dataset comprises Soil Temperature and Deformation monitoring data gathered from a watershed situated along the Nome-Teller road at Mile 47 in Alaska. Its primary objective is to enhance comprehension of deformation mechanisms in permafrost environments by using 51 probes designed following Wielandt et al. (2022). The dataset comprises a description of Probe_ID, Location, start time, end time and probe length in the "ProbesLocations_StartEndDates.csv" file, the 51 data files encapsulated within "Data_files.zip" and the computed deformation for 2023 and 2022 in "Deformation_T47.zip".Each file in Data_files.zip is named as followed "ProbeId_StartMonth_EndMonth.csv". Within each file, the initial column denotes the timestamp in UTC, followed by the sensor’s battery voltage and temperature and acceleration values (X, Y, Z) in subsequent columns. The data collection frequency is set at 30-minute intervals. Each file in Deformation_T47.zip is named as followed "ProbeId_Temp_def_year.csv". Within each file, the initial column denotes the timestamp in UTC, followed by the temperature at each sensor and cumulative deformation from last to first sensor in subsequent columns. The data collection is daily averaged.This dataset forms an integral component of the Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic). 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

Greenhouse Gas Production and Soil Chemistry in Anaerobic Soil Microcosm Incubations after Nitrogen Addition, Teller Road Site, Seward Peninsula, 2018-2019

This dataset provides the results of laboratory soil microcosm incubation experiments conducted under anaerobic conditions with and without the addition of ammonium chloride (NH4Cl). The microcosms contained soil collected in April 2017 from the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) near Intensive Site 9 (Toeslope) and Intensive Site 5 (Plateau). Incubations were conducted at 8°C for 55 days, with repeated measurements of headspace greenhouse gas concentrations. Microcosms were destructively harvested and extracted using ultrapure water and 0.1 M KCl for analysis of the porewater geochemistry. This dataset contains two csv files, a pdf user guide. and the raw data in a zip file.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 OSTI2021

Reactive oxygen species alter chemical composition and adsorptive fractionation of soil organic matter

Reactive oxygen species (ROS), formed during redox fluctuations in iron-rich soils, have been known to stimulate lignin degradation, although not much is known about how they alter soil organic matter (SOM) composition and interaction with mineral surfaces. We conducted a laboratory experiment to see how ROS altered SOM composition and adsorptive fractionation onto Fe-mineral surfaces. We reacted water extracts of SOM with ·OH, produced by the Fenton reaction, and then conducted a sorption experiment of the extracts with goethite to analyze the amount and quality of SOM adsorbed. The Fenton reaction preferentially consumed low-O, mostly aromatic molecules, and new high-O molecules were detected post-Fenton, nearly half of which were carbohydrate-like. Although the amount of C adsorbed did not change after oxidation, the post-Fenton adsorbed molecules were more oxidized. Pre-Fenton adsorption was dominated by aromatic molecules (90%), but post-Fenton, the adsorbed molecules were 75% aromatic and 25% carbohydrate-like. We show that the ·OH radical oxidized SOM and shifted patterns of adsorption to a more oxidized pool. Because adsorption to minerals is thought to stabilize SOM, our results suggest that ROS may alter the availability and stabilization patterns of SOM.

Patel, Kaizad F.↗
DOE OSTI2022

Microbe-iron interactions control lignin decomposition in soil

Lignin decomposition is critically linked to terrestrial carbon (C) cycle due to the enormous C mass of lignin and its importance in controlling overall rates of litter decomposition. Interactions between lignin and iron (Fe) minerals have been increasingly recognized as key mediators of lignin decomposition in experimental studies. However, we still lack a quantitative understanding of how Fe minerals interact with microbes to control lignin decomposition. Here, we leveraged experimental results from an incubation of Fe-rich soil, in which lignin decomposition rates were measured at aerobic conditions after four levels of pre-treated O2 availability, to examine microbe-Fe (MiFe) interactions in lignin decomposition with a MiFe model. We quantified how Fe redox cycling interacted with microbial activities to control lignin decomposition via data-model integration. Our results showed that the MiFe model with time-dependent growth and mortality functions better represented CO2 release from lignin decomposition (R2 ranging from 0.96 to 0.97) than models assuming either first-order or Michaelis-Menten kinetics. Reduction of Fe(III) to Fe(II) after pre-treatments with lower O2 availability stimu-lated the Fenton reaction to break down macro-molecular lignin into small molecules available to microbes. The small molecules of lignin and necromass bounded with oxidized Fe and were protected from decomposition. After 1-year incubation, the model implied that most of C stabilized with Fe minerals was derived from small molecular lignin C. Our quantitative analysis of microbe-Fe interactions sheds new light on lignin decomposition and preservation and helps improve model prediction of soil C persistence under global change.

Liao, Cuijuan↗
DOE OSTI2022

Effects of fine-root senescence upon soil communities and nutrient flux into soil pools (Final Report)

Fine roots represent an important flux of carbon into terrestrial soils. Much of this flux occurs through the exudation of polysaccharides and other carbon compounds during the lifetime of fine-roots, but little is known about their contributions to flux as roots senesce, die and decompose. This project was designed 1) to test approaches for inducing senescence in fine roots and 2) assess the effects of the treatments on fine roots and the associated rhizosphere community. We implemented two fine-root treatments, a steam girdling approach and full severing of fine root modules from the tree, and we contrasted them with a control where roots were handled but not girdled. Fine roots and their associated community subjected to each of these three treatments were subsequently analyzed for changes in physical structure, nutrient content, community structure and gene function. Both girdling manipulations resulted in tissue disruption in fine roots and changes in the soil community relative to controls. In particular, microbial diversity for most taxa declined in girdled treatments whereas fungal diversity increased. We also observed changes in overall plant and fungal gene expression associated with treatment with plant gene expression declining over time in girdled roots with a simultaneous increase in fungal gene expression in these same treatments. Finally, in girdled fine root modules, we observed changes in gene function associated with senescence and plant stress in pine-associated genes while at the same time observing upregulation of genes associated with growth and proliferation in fungi. In conclusion, we were able to successfully girdle fine-roots in a field setting and resolve plant-level and community level changes in response to these girdling treatments.

54 ENVIRONMENTAL SCIENCES↗