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18 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The importance of accounting for landscape position when investigating grasslands: A multidisciplinary characterisation of a Californian coastal grassland

Data from the characterisation of the Point Reyes Field Site, published in AGU Earth's Future under the title: The importance of accounting for landscape position when investigating grasslands: A multidisciplinary characterisation of a Californian coastal grassland. This paper explored the effect of landscape position on the response of a Californian grassland to seasonal changes. All files are csv files. The EMI data contains 8 csv files with a metadata csv explaining the columns. The dataset also includes soil variables including total concentrations calculated from fused samples, then dissolved and measured on ICP-AES for whole-rock elements and ICP-MS for trace elements. Mineral composition was attained using X-ray diffraction at BL 11-3 at SSRL . Data was then run through the High Score database to characterise different mineral phases. total It also includes a table with bulk soil characteristics such as soil pH, cation exchange capacity, and soil textural data. Data from Teros 12 Meter soil moisture, electrical conductivity and temperature sensors are presented in SMS Csv file. While the WL bottom and top files contain data from Piezometers measuring the ground water table. We have included a csv file that contains soil CO2 efflux data from Feb 2021-Oct 2021 in the Point Reyes Grassland Experiment We have included the spatially orientated (easting northing) remotely sensed datasets that were used in the K-means clustering analysis conducted on our site with electrical conductivity, normalised difference vegetation index, elevation, slope, solar radiation, topographic position and wetness index, and a clustering score. Finally there is a list of all the identified grassland species at the site.For more information on flux data, please contact the corresponding author.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Association between soil organic carbon and calcium in acidic grassland soils from Point Reyes National Seashore, CA

All data is collected from across 3 soil cores spanning a pH gradient at Point Reyes National Seashore, as part of a recent publication. The bulk data csv includes hygroscopic moisture content, soil pH, total C and N values, particle size distributions, cation exchange capacity and extractable cations. The STXM data package includes raw spectra data from scanning transmission X-ray microscopy C near-edge X-ray absorption fine structure spectroscopy analysis, extracted from STXM Image Reader analysis and then subsequently normalised in Athena (see details in paper). The data file also contains a bulk chemistry and mineralogy dataset, including total and trace element contents from 3 depths and mineral compositions as measured at BL 11-3 SSRL and semi-quantified in HighScore. Finally the final data file is calcium K-edge X-ray absorption near-edge structure spectroscopy (BL 4-3) and micro-XANES and micro-X-ray fluorescence (BL 14-3b) data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Rhizosphere Soil Biogeochemical Data and Photosynthetic Data of Vicia Faba in a Rhizobox

Here we share the data in column format via csv files for pH, redox, and dissolved oxygen collected at hourly resolution from microelectrodes. Dissolved organic carbon concentrations collected from TOC are also provided in a similar format but are composited samples from hourly microdialysis collection. This provided resolution of diel rhizosphere dynamics belowground. Plant physiological data was also collected at every 5 min for 24 hr cycles in order to capture diel dynamics aboveground. This data was used to parameterize the reaction transport model eSTOMP-ROOTS, which examines the rhizosphere biogeochemistry of a growing Vicia faba plant. The aim was to investigate plant activity and belowground biogeochemical processes, particularly their impact on mineral-organic associations in the rhizosphere. We combined in-situ rhizosphere microsensor and plant physiological measurements with a 3-D plant-soil reactive transport model to explore the behavior of dissolved organic carbon (DOC) in the rhizosphere. Over several days, microdialysis probes placed at the root-soil interface in live soil showed distinct daily patterns of DOC concentration in the pore water. Spikes in DOC concentrations during the day aligned with peaks in leaf-level photosynthesis, accompanied by decreasing redox potential and dissolved oxygen levels, and increasing pH in the rhizosphere. This new mechanistic modeling framework, which integrates aboveground plant physiological data with non-destructive, high-resolution monitoring of rhizosphere processes, offers significant potential for studying the factors that control carbon storage in soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Heating effects on jack pine pyrogenic organic matter properties from a pyrocosm study in 2022

This dataset contains data associated with the preprint “Fire removes preexisting pyrogenic organic matter from the ecosystem through the mechanisms of both direct combustion and increasing mineralizability” (Luo et al., 2025b), which is the complementary study to the published paper “Reburning pyrogenic organic matter: a laboratory method for dosing dynamic heat fluxes from above” (Luo et al., 2025a). We designed a full-factorial experiment with different burial depths of jack pine (Pinus banksiana Lamb) pyrogenic organic matter (PyOM) (Surface, 1 cm, and 5 cm) and different heat-flux profiles (High, Low, and Control) to examine how subsequent fires affect the properties of preexisting PyOM. We measured total carbon (C), pH, dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), and mineralized C (as CO₂-C, from a 12-week incubation).We found that high heat flux and/or surface placement resulted in substantial direct C losses through combustion. Intermediate heat exposure produced both combustion losses and increases in DOC and mineralizability, which may have complex long-term implications: an increased dissolved fraction of PyOM may promote downward transport into mineral soils and potentially contribute to deeper, longer-term C storage, but it may also make PyOM more susceptible to microbial decomposition. Under the lowest heat flux and deepest burial, most PyOM was retained, and changes in DOC and C mineralization were minimal. Finally, PyOM pH, an important chemical property, decreased under low-temperature heating but increased under higher temperatures.We uploaded pH data for all samples (“pH_of_all_samples.csv”); pH and temperature-related data (peak temperature and degree hours) for samples in High and Low heat-flux treatments (“pH_vs_peakT_and_degree_hours_only_for_heated_samples.csv”); total C data (“CN_pct_C_stock_C_loss_in_samples.csv”); DOC and DIC data (“doc_dic.csv”); and mineralized C (CO₂-C) data (“CO2-C_all_original.csv”). Additional details can be found in the Methods & Sampling section.All datasets uploaded to ESS-DIVE are clearly labeled, cleaned, and include both raw and derived data, ready for reuse in other analyses. All analysis code and raw datasets are also available on GitHub: https://github.com/MengmengLuo/Fire-removes-preexisting-pyrogenic-organic-matter-from-the-ecosystem.

54 ENVIRONMENTAL SCIENCES↗
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 OSTI2025

Calcium is associated with specific soil organic carbon decomposition products at Blodgett Forest Research Center, Georgetown, California as analysed with scanning transmission X-ray microscopy carbon near-edge X-ray absorption fine structure spectroscopy

This data is from the paper calcium is associated with specific soil organic carbon decomposition products, published in SOIL. DOI: https://doi.org/10.5194/soil-11-381-2025, 2025.This file contains CSVs with spectral data and bulk soil data and there is no specific program required to open this data. The data includes Scanning transmission X-ray microscopy carbon near-edge X-ray absorption fine structure spectroscopy. data from the measurement of samples from the Whole-soil Warming project, run by the Belowground Biogeochemistry team at Blodgett Forest Research Center, Georgetown, California run by the University of California, Berkeley. It also includes bulk soil chemical properties. The University of California's Blodgett Forest Research Station (Forest) is situated in the Sierra Nevada foothills (1370 m a.s.l.) near Georgetown, California. The samples were collected from here: 38.912013, -120.661469, https://maps.app.goo.gl/291bCJ1zVqUhgktz6. The Forest soils were characterised as Alfisols, which are equivalent to Dystric Cambisols (IUSS Working Group WRB, 2015), and formed in granitic parent materials, in a temperate climate, under thinned, mixed-coniferous forest (Fig. S3; Gaudinski et al., 2009). With these analyses we aimed to answer the question, is calcium associated with a specific type of organic matter enriched in aromatic and phenolic carbon at the microscale in samples from Blodgett Forest Research Center? and how does this specific type of carbon respond to experiments targetted at removing and adding calcium to the soils, specifically cation exchange and incubation after calcium addition? Abstract from the paper can be found below: Calcium (Ca) may contribute to the preservation of soil organic carbon (SOC) in more ecosystems than previously thought. Here we provide evidence that Ca is co-located with SOC compounds that are enriched in aromatic and phenolic groups, across different acidic soil-types and locations with different ecosystem properties, differing in terms of climate, parent material, soil type, and vegetation. In turn, this co-localised fraction of Ca-SOC is removed through cation-exchange, and the association is then only re-established during decomposition in the presence of Ca (Ca addition incubation). Thus, highlighting a causative link between decomposition and the co-location of Ca with a characteristic fraction of SOC. Decomposition increases the relative proportion of negatively charged functional groups, which can increase the propensity for the association between SOC and Ca, and in turn, this association inhibits dissolved organic carbon export or further decomposition. We propose that this mechanism could be driven by Ca hotspots on the microscale shifting local decomposition processes and thereby explaining the colocation of Ca with SOC of a specific composition across different acidic soil environments. Incorporating this biogeochemical process into Earth System Models could improve our understanding, predictions, and management of carbon dynamics in soils, and account for their response to Ca-rich amendments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Evaluating the Persistence of Soil Carbon After a 30-Year Nitrogen Fertilization Experiment at the Fernow Experimental Forest, WV

We sampled soils in a previously nitrogen (N)-fertilized watershed (Watershed 3), which received 35 kg N per hectare annually for 30 years, and a reference watershed (Watershed 7), 4 years after the end of a 30-year N fertilization experiment at the Fernow Experimental Forest in West Virginia. As N deposition has reduced soil pH and plant carbon (C) investments into the rhizosphere, we compared the extent to which removing these potential limitations to microbial decomposition by increasing soil pH, adding artificial root exudates, or elevating soil temperature would increase microbial decomposition (and soil C losses) in soils that have and have not received excess N inputs. As such, we incubated soils with and without the addition of artificial root exudates and dolomitic lime (2 amendment treatments and 1 untreated control), at three different temperatures (15, 20, and 25 C) to simulate warming. We measured soil respiration, enzyme activity (acid phosphatase, N -acetyl-β-glucosaminidase, beta-glucosidase, phenol oxidase, and peroxidase), and microbial biomass carbon in a 15-week microcosm experiment. All of the datasheets include the metadata for all of the treatment combinations from this incubation experiment (ID, incubation temperature, treatment, watershed).The "Soil_Chemistry_Data.csv" data includes (1) the ratio of dry soil weight (g) by wet (or fresh) soil weight (g) after 72 hours at 65 C, (2) the wet (or fresh) weight of the soil samples used to determine soil pH, and (3) soil pH, which was measured in CaCl2. Detailed methods for the measurements of soil pH are described in the datasheet itself.The "Respiration_Data.csv" data includes (1) respiration day for the measurement, and (2) cumulative CO2 respiration (mmol) measured in the microcosms on specific days.The "Microbial_Biomass_Data.csv" data includes (1) mmol microbial biomass carbon per g (dry weight) of soil in each microcosm.The "Enzyme_Data.csv" data includes (1) all extracellular soil enzyme activity (N-acetyl-glucosaminidase (NAG), acid phosphatase (AP), β-glucosidase (BG), phenol oxidase and peroxidase) that we measured in our microcosms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

EXCHANGE Campaign Degradation (ECD): Understanding Decomposition Dynamics Across Mid-Atlantic and Great Lakes Coastal Ecosystems

The EXploration of Coastal Hydrobiogeochemistry Across a Network of Gradients and Experiments (EXCHANGE) Degradation Experiment (EXCHANGE-D) is an in situ experiment designed to assess organic matter decomposition rates across coastal terrestrial-aquatic interfaces (TAIs), from coastal uplands through transition zones to wetlands. Through a network of partner scientists and coastal sites, we are testing how environmental gradients shape decomposition and carbon dynamics across terrestrial-aquatic interfaces. Using standardized tea bag substrates deployed across a network of diverse coastal sites, we compare decomposition rates at different fresh- and salt-water TAIs to develop transferable knowledge that improves the representation of organic matter degradation in coastal ecosystem models. For more information, please see https://compass.pnnl.gov/FME/EXCHANGE. This is Version 1 of the data package, which includes: ecd_README.pdf flmd.csv dd.csv ecd_soil_weom_L2.csv ecd_soil_ph_conductivity_L2.csv ecd_soil_gwc_L2.csv ecd_soil_teabag_degradation_L2.csv ecd_readme.pdf

coastal soils↗
DOE OSTI2024

Soil Carbon Dynamics Following Land Use Changes and Conversion to Oil Palm Plantations in Tropical Lowlands Inferred From Radiocarbon

We measured the 14C and 13C isotopic values of soil organic carbon in mineral soil from lowland tropical forests to provide insight into how quickly carbon is turning over in the soil following conversion of primary forests to oil palm plantations. In addition to areas converted to oil palm plantations in Peru, Indonesia, and Cameroon, we examine pastures and secondary forests in Peru as a comparison to the carbon cycling processes operating in the oil palm plantations.This dataset includes radiocarbon (Δ14C) and stable carbon (δ13C) isotopes of soil organic carbon in mineral soils from natural lowland forests and oil palm plantations in Peru, Indonesia, and Cameroon. We additionally examine plots of secondary forests following agricultural use and pastures on cleared natural forest in Peru. In addition to isotopic data, this dataset includes soil carbon and nitrogen concentrations and stock, soil texture (percent sand, silt, and clay), pH, ECEC (effective cation exchange capacity), base saturation, and bulk density. Soils were sampled in 4 depth increments to 100 cm depth.This dataset supports the publication Finstad et al., 2020. Finstad, K., van Straaten, O., Veldkamp, E., & McFarlane, K. (2020). Soil carbon dynamics following land use changes and conversion to oil palm plantations in tropical lowlands inferred from radiocarbon. Global Biogeochemical Cycles, 34, e2019GB006461. https://doi.org/10.1029/2019GB006461

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Data from: 'Abiotic influences on continuous conifer forest structure across a subalpine watershed'

This package archives the core data used for analysis and inference in 'Abiotic influences on continuous conifer forest structure across a subalpine watershed' (Worsham et al., 2025). All data were collected in the East River, Washington Gulch, Slate River, and Coal Creek watersheds of Colorado. In the paper, we quantified the relative influence of climate, topographic, edaphic, and geologic factors on conifer stand structure and composition, and their functional relationships, at the watershed scale. We used waveform LiDAR data to derive spatially continuous stand structure metrics. We fused these with a species-level classification map to estimate tree species abundance. We applied generalized additive and generalized boosted models to evaluate the covariability of structural and compositional metrics with abiotic variables. The package contains the essential products required for reproducing our analysis and the tables and figures reported in the publication. The products comprise four classes: (1) geospatial data, (2) tabular data used for inferential analysis, (3) tabular data describing analytical results and performance statistics, and (4) a data user guide. (1) includes discretized waveform LiDAR data, locations and attributes of individual tree crowns, sampling locations and domain boundaries, a canopy height model, and raster files of estimated forest structural and compositional metrics at 100 m grid scale. (2) includes all response and explanatory variable values applied in inferential models. Response variables include conifer forest stand density, basal area, 95th percentile height, quadratic mean diameter, and others. Explanatory variables include climatic water deficit, actual evapotranspiration, elevation, heat load, soil available water content, and others. (3) includes results of training and testing several individual tree detection (ITD) algorithms, as well as inferential modeling results. (4) is a PDF user guide for this data package, including detailed descriptions and data dictionaries for all files. The data package root contains 17 assets: 8 compressed tape archive (.tar.gz) files, 5 comma-separated values (.csv) files, 3 Geographic Tagged Image File Format (GeoTIFF) (.tif) files, and 1 Portable Document Format (.pdf) file. The compressed .tar.gz archives contain ESRI shapefiles (.shp) .tif, compressed LASer (.laz), and .csv files. The archives must first be decompressed using the widely distributed command-line software utility TAR. All other files, including constituent files within the .tar.gz archives, can be opened in the open-source R statistical computing environment. Alternatively, .csv files may also be read in any simple text editor software or Microsoft Excel. Geospatial files including .shp and .tif files can also be opened in GIS software, such as QGIS (open-source) or ESRI ArcGIS (proprietary). The .pdf Data User Guide can be read with Adobe Acrobat Reader or other compatible readers.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2026

Patch-level CO2 and CH4 fluxes and porewater concentrations in experimental wetlands, 5 and 10 PPT saltwater intrusion simulations, Louisiana 2023-2024

This dataset containes carbon dioxide (CO2) and methane (CH4) flux measurements collected from wetland vegetation patches dominated by Typha domingensis and Panicum hemitomon to assess greenhouse gas flux responses to experimental saltwater intrusion (SWI) pulses. Measurements were conducted before, during, and after simulated SWI events at target salinities of approximately 5 parts per thousand (ppt) with durations of 6, 10, and 17 days and 10 ppt with a duration of 48 days, alongside a control wetland (with no salinity added, flood manipulation only). These data were generated to evaluate how the magnitude and duration of SWI alter wetland carbon exchange and related biogeochemical and plant responses. This data package includes flux measurements from the wetland surface (i.e, soil/water surface and enclosed vegetation) and from the soil/water surface only; porewater and surface water concentrations of CO2 and CH4; salinity, pH, electrical conductivity collected in porewater (at 5, 10, and 20 cm soil depths) and in surface water; soil redox potential; leaf spectral indices, leaf vapor pressure deficit, stomatal conductance; water level, salinity, and photosynthetically active radiation; and aboveground biomass.

EARTH SCIENCE > AGRICULTURE > SOILS > SOIL RESPIRA↗
DOE OSTI2020

Black carbon enriches short-range-order ferrihydrite in Amazonian Dark Earth: Interplay mechanism and environmental implications

Our study underpins the mechanism of organo-mineral interaction between black carbon (BC, biochar) and associated minerals in the historical BC-rich Amazonian Dark Earth (ADE) by using synchrotron-based microscopic (TXM), microspectroscopic (μFTIR) and spectroscopic (XAS and μ-diffraction) approaches. The BC-rich ADE contained over 100% more poorly crystalline minerals than the adjacent tropical soil. Linear combination fitting of k-spacing in the X-ray Absorption Spectra (XAS) revealed that ferrihydrite contributed to 81.1% of the Fe-minerals in BC. A small but distinct peak was observed at 5.7 Å –1 in the extended X-ray absorption fine structure k oscillation of BC, revealing the presence of Fe—C (including Fe-O-C) covalent bonds. No Fe—C path was yielded by the XAS fitting when an obvious peak downshift of the first (Fe—Fe 1 ) shell was observed, suggesting that the availability of inner-sphere Fe—C complexation was limited to the BC surface and interphase region. In this study, the main minerals for organo-mineral complexation were short-range-order (SRO) ferrihydrite on BC instead of corner-sharing FeO 6 octahedra. Compared to ADE, the coordination number of the first (Fe—Fe 1 ) and second (Fe—Fe 2 ) shell was higher in BC, revealing a higher degree of order in coordination between the neighboring Fe mineral crystals. Black C limited the progressive aging of amorphous Fe phases and greatly enriched SRO ferrihydrite in the redox-fluctuating and high-leaching environment. The transformation of SRO ferrihydrite into the more crystalline Fe oxides was controlled by the local pH environment. A strong signal from the complexed phenolic group (aryl-OH, 1241 cm –1 ) and a distinct band of inner-sphere complexation (Fe-aryl C, 1380–1384 cm –1 ) were identified in the FTIR spectra. The enrichment of poorly crystalline minerals can have positive feedback on the long-term stabilization of BC. The scale-up application of biochar to agricultural and ecological systems may have a long-lasting impact on the enrichment and transformation of the SRO minerals in the soil.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Untargeted metabolite data from a root surface in a rhizobox

Raw data is provided from samples analyzed using separate reverse phase chromatographic methods on a high performance liquid chromatograph with mass spectrometry. These porewater samples were collected from a microdialysis which generated samples along the surface of a growing A. sative root (all_hc). This data was used to answer questions connecting rhizosphere metabolite (putatively identified metabolites, hc_putative_norm) changes over time (root growth) with changes in the surrounding rhizosphere biogeochemistry (DOC, redox, pH). Rhizosphere biogeochemistry values are provided in the hc_putative_norm file as averages over their respective range of time that they were collected at. The hc_putative_norm file also contains all normalized values over only the intensity values collected for putatively identified metabolites.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Data for: A Synoptic System for Capturing Ecosystem Control Points Across Terrestrial-Aquatic Interfaces

The investigation of how climate change and water level fluctuations impact variable and interconnected ecosystems, like the interfaces between terrestrial and aquatic environments, requires the collection and integration of many data types. We describe an integrative and autonomous environmental monitoring approach that uses environmental sensors and data loggers to monitor surface water, groundwater, soil, and vegetation changes and generate essential data for predictive models. We established the network at seven sites along the Chesapeake Bay and Lake Erie coastlines, including a large-scale flood manipulation experiment, collectively generating over three million observations per month. Such sensor networks hold great promise for tracking and comprehending environmental changes where land and water intersect. The sensor system and overall approach to sensor management that we have designed is intended to be widely accessible for research teams spanning in size from an individual investigator to large multi-institution projects. This dataset shows example data generated by the sensor network described above. Data output for data loggers connected to groundwater water quality sondes measuring dissolved oxygen, pH, oxidative redox potential (ORP), groundwater elevation, groundwater salinity and temperature, and groundwater elevation; replicate soil moisture and conductivity probes installed at 10 and 30 cm below the ground surface; rainfall and solar radiation; and mean sap flow from 8 replicate probes. Sensors are installed at upland forest (UP), wetlands (W), and transitional locations between these ecosystems (TR). Example datasets are from Goodwin Islands in the Chesapeake Bay and Portage River along the Lake Erie coastline.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.

16S rRNA gene amplicon Illumina sequencing↗
DOE OSTI2024

Nitrogen Deposition Weakens Soil Carbon Control of Nitrogen Dynamics Across the Contiguous United States

ABSTRACT Anthropogenic nitrogen (N) deposition is unequally distributed across space and time, with inputs to terrestrial ecosystems impacted by industry regulations and variations in human activity. Soil carbon (C) content normally controls the fraction of mineralized N that is nitrified ( ƒ nitrified ), affecting N bioavailability for plants and microbes. However, it is unknown whether N deposition has modified the relationships among soil C, net N mineralization, and net nitrification. To test whether N deposition alters the relationship between soil C and net N transformations, we collected soils from coniferous and deciduous forests, grasslands, and residential yards in 14 regions across the contiguous United States that vary in N deposition rates. We quantified rates of net nitrification and N mineralization, soil chemistry (soil C, N, and pH), and microbial biomass and function (as beta‐glucosidase (BG) and N ‐acetylglucosaminidase (NAG) activity) across these regions. Following expectations, soil C was a driver of ƒ nitrified across regions, whereby increasing soil C resulted in a decline in net nitrification and ƒ nitrified . The ƒ nitrified value increased with lower microbial enzymatic investment in N acquisition (increasing BG:NAG ratio) and lower active microbial biomass, providing some evidence that heterotrophic microbial N demand controls the ammonium pool for nitrifiers. However, higher total N deposition increased ƒ nitrified , including for high soil C sites predicted to have low ƒ nitrified , which decreased the role of soil C as a predictor of ƒ nitrified . Notably, the drop in contemporary atmospheric N deposition rates during the 2020 COVID‐19 pandemic did not weaken the effect of N deposition on relationships between soil C and ƒ nitrified . Our results suggest that N deposition can disrupt the relationship between soil C and net N transformations, with this change potentially explained by weaker microbial competition for N. Therefore, past N inputs and soil C should be used together to predict N dynamics across terrestrial ecosystems.

Nieland, Matthew A. [Stockbridge School of Agricul↗
DOE OSTI2026

Marginal Soils Index Analysis & Geospatial Data

This data package contains output files associated with the Mongird et al. paper entitled "Can US power grid expansion avoid prime agricultural lands?" and is organized into four dataset directories. Each dataset is described in more detail below. 1. Marginal Soils Index Analysis Description: This folder contains a csv file with land needs and availability by state, power generating technology type, and scenario in 2050 when suitable siting areas are additionally constrained to areas with increasing levels of soil marginality. Files: msi_constrained_siting_availability_2050.csv Variables: Scenario - Projected 2050 scenario name State - US state abbreviation Technology - Generating technology type solar = solar photovoltaic gas_cc_re = natural gas combined cycle (recirculating cooling) wind = onshore wind gas_cc_ccs_re = natural gas combined cycle with carbon capture sequestration (recirculating cooling) gas_cc_dry = natural gas combined cycle with (dry cooling) gas_cc_pond = natural gas combined cycle with (pond cooling) coal_conv_ccs_re = conventional coal with carbon capture sequestration (recirculating cooling) Req_Capacity_MW - The amount of rated capacity required in 2050 of the given technology type in the given state and under the given scenario from the capacity expansion plan Req_Capacity_Factor - The assumed capacity factor (fraction between 0 and 1) for the given technology type in the given state and under the given scenario by the capacity expansion plan Req_Land_km2 - The amount of land required (in km-squared) to host the required generating capacity that is capable of meeting the specified capacity factor for the given technology type in the given state and under the given scenario Req_Energy_TWh - Product of Req_Capacity_MW, Req_Capacity_Factor, and 8760/1e6 for the given technology type in the given state and under the given scenario MSI_Case - The level of MSI that siting the given technology is additionally constrained to, where >0 means siting is additionally constrained to suitable land areas that have an MSI value greater than 0 >=1 means siting is additionally constrained to suitable land areas that have an MSI value greater than or equal to 1 >=2 means siting is additionally constrained to suitable land areas that have an MSI value greater than or equal to 2 >=3 means siting is additionally constrained to suitable land areas that have an MSI value greater than or equal to 3 Soil Attribute Rasters Description: This folder contains geospatial raster files for individual soil parameters upscaled to the listed grid resolution (30m or 1 km). 1 km resolution files are a spatial average of non-missing 30m resolution values. All raster files use the USA Contiguous Albers Equal Area Conic (ESRI:102003) projection. Files: avg_cond_raster_ .tif - Average conductivity of the saturation extract across all soil horizons within a depth of 40 inches, measured in mmhos/cm max_cond_raster_ .tif - Maximum conductivity of the saturation extract across all soil horizons within a depth of 40 inches, measured in mmhos/cm min_ph_raster_ .tif- Min pH values across all soil horizons within a depth of 40 inches. avg_ph_raster_ .tif - Average pH value across all soil horizons within a depth of 40 inches. max_ph_raster_ .tif- Max pH value across all soil horizons within a depth of 40 inches. erosion_factor_raster_ .tif - Product of k-factor and percent slope flood_freq_raster_ .tif - Number of months of the year during which the area is commonly, frequently, or very frequently flooded. max_sar_raster_ .tif - Maximum sodium adsorption ratio across all horizons within a depth of 40 inches rock_frac_raster_ .tif - Fraction of the upper 6 inches of soil composed of rock fragments larger than 3 inches. temp_regime_raster_ .tif - Soil temperature regime with the following key: 0 = pergelic 1 = gelic 2 = cryic 3 = frigid 4 = isofrigid 5 = mesic 6 = isomesic 7 = thermic 8 = isothermic 9 = hyperthermic 10 =isohyperthermic Marginal Soils Index Rasters Description: This folder contains geospatial raster files of the Marginal Soils Index at the listed grid resolution (30m or 1 km). 1 km resolution files are a spatial average of 30m resolution. Both raster files use the USA Contiguous Albers Equal Area Conic (ESRI:102003) projection. A value of 0 indicates that there were no soil attributes present that indicate marginal soil. NA values indicate that data was unavailable or bodies of water. Files: marginal_soils_index_30m_raster.tif marginal_soils_index_1km_raster.tif Marginal Soils Index Resource Potential Rasters Description: This folder contains geospatial raster files of the Marginal Soils Index + Resource Potential (MSIxRP) score at 1km resolution for geothermal, solar, and wind technologies. Raster files use the USA Contiguous Albers Equal Area Conic (ESRI:102003) projection. NA values indicate that the location is not suitable for siting the given technology due to policy, environmental, socioeconomic, topological, and other constraints regardless of soil marginality level. Areas with values greater than or equal to zero represent the product of the normalized MSI value and the normalized resource potential value. Files: geothermal_msi_rp_score_raster.tif solar_msi_rp_score_raster.tif wind_msi_rp_score_raster.tif Acknowledgment IM3 is a multi-institutional effort led by Pacific Northwest National Laboratory and supported by the U.S. Department of Energy's Office of Science as part of research in MultiSector Dynamics, Earth and Environmental Systems Modeling Program. Disclaimer This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor the Contractor, nor any or their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. PACIFIC NORTHWEST NATIONAL LABORATORYoperated byBATTELLEfor theUNITED STATES DEPARTMENT OF ENERGYunder Contract DE-AC05-76RL01830

Agriculture↗
DOE OSTI2026

Marginal Soils Index Analysis & Geospatial Data

This data package contains output files associated with Mongird et al. (in prep) organized into four dataset directories. Each dataset is described in more detail below. 1. Marginal Soils Index Analysis Description: This folder contains a csv file with land needs and availability by state, power generating technology type, and scenario in 2050 when suitable siting areas are additionally constrained to areas with increasing levels of soil marginality. Files: msi_constrained_siting_availability_2050.csv Variables: Scenario - Projected 2050 scenario name State - US state abbreviation Technology - Generating technology type solar = solar photovoltaic gas_cc_re = natural gas combined cycle (recirculating cooling) wind = onshore wind gas_cc_ccs_re = natural gas combined cycle with carbon capture sequestration (recirculating cooling) gas_cc_dry = natural gas combined cycle with (dry cooling) gas_cc_pond = natural gas combined cycle with (pond cooling) coal_conv_ccs_re = conventional coal with carbon capture sequestration (recirculating cooling) Req_Capacity_MW - The amount of rated capacity required in 2050 of the given technology type in the given state and under the given scenario from the capacity expansion plan Req_Capacity_Factor - The assumed capacity factor (fraction between 0 and 1) for the given technology type in the given state and under the given scenario by the capacity expansion plan Req_Land_km2 - The amount of land required (in km-squared) to host the required generating capacity that is capable of meeting the specified capacity factor for the given technology type in the given state and under the given scenario Req_Energy_TWh - Product of Req_Capacity_MW, Req_Capacity_Factor, and 8760/1e6 for the given technology type in the given state and under the given scenario MSI_Case - The level of MSI that siting the given technology is additionally constrained to, where >0 means siting is additionally constrained to suitable land areas that have an MSI value greater than 0 >=1 means siting is additionally constrained to suitable land areas that have an MSI value greater than or equal to 1 >=2 means siting is additionally constrained to suitable land areas that have an MSI value greater than or equal to 2 >=3 means siting is additionally constrained to suitable land areas that have an MSI value greater than or equal to 3 Soil Attribute Rasters Description: This folder contains geospatial raster files for individual soil parameters upscaled to the listed grid resolution (30m or 1 km). 1 km resolution files are a spatial average of non-missing 30m resolution values. All raster files use the USA Contiguous Albers Equal Area Conic (ESRI:102003) projection. Files: avg_cond_raster_ .tif - Average conductivity of the saturation extract across all soil horizons within a depth of 40 inches, measured in mmhos/cm max_cond_raster_ .tif - Maximum conductivity of the saturation extract across all soil horizons within a depth of 40 inches, measured in mmhos/cm min_ph_raster_ .tif- Min pH values across all soil horizons within a depth of 40 inches. avg_ph_raster_ .tif - Average pH value across all soil horizons within a depth of 40 inches. max_ph_raster_ .tif- Max pH value across all soil horizons within a depth of 40 inches. erosion_factor_raster_ .tif - Product of k-factor and percent slope flood_freq_raster_ .tif - Number of months of the year during which the area is commonly, frequently, or very frequently flooded. max_sar_raster_ .tif - Maximum sodium adsorption ratio across all horizons within a depth of 40 inches rock_frac_raster_ .tif - Fraction of the upper 6 inches of soil composed of rock fragments larger than 3 inches. temp_regime_raster_ .tif - Soil temperature regime with the following key: 0 = pergelic 1 = gelic 2 = cryic 3 = frigid 4 = isofrigid 5 = mesic 6 = isomesic 7 = thermic 8 = isothermic 9 = hyperthermic 10 =isohyperthermic Marginal Soils Index Rasters Description: This folder contains geospatial raster files of the Marginal Soils Index at the listed grid resolution (30m or 1 km). 1 km resolution files are a spatial average of 30m resolution. Both raster files use the USA Contiguous Albers Equal Area Conic (ESRI:102003) projection. A value of 0 indicates that there were no soil attributes present that indicate marginal soil. NA values indicate that data was unavailable or bodies of water. Files: marginal_soils_index_30m_raster.tif marginal_soils_index_1km_raster.tif Marginal Soils Index Resource Potential Rasters Description: This folder contains geospatial raster files of the Marginal Soils Index + Resource Potential (MSI+RP) score at 1km resolution for geothermal, solar, and wind technologies. Raster files use the USA Contiguous Albers Equal Area Conic (ESRI:102003) projection. NA values indicate that the location is not suitable for siting the given technology due to policy, environmental, socioeconomic, topological, and other constraints regardless of soil marginality level. Areas with values greater than or equal to zero represent the product of the normalized MSI value and the normalized resource potential value. Files: geothermal_msi_ep_score_raster.tif solar_msi_ep_score_raster.tif wind_msi_ep_score_raster.tif Acknowledgment IM3 is a multi-institutional effort led by Pacific Northwest National Laboratory and supported by the U.S. Department of Energy's Office of Science as part of research in MultiSector Dynamics, Earth and Environmental Systems Modeling Program. Disclaimer This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor the Contractor, nor any or their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. PACIFIC NORTHWEST NATIONAL LABORATORYoperated byBATTELLEfor theUNITED STATES DEPARTMENT OF ENERGYunder Contract DE-AC05-76RL01830

Agriculture↗