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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Sample Identifiers and Metadata Reporting Format for Environmental Systems Science

The ESS-DIVE sample identifiers and metadata reporting format primarily follows the System for Earth Sample Registration (SESAR) Global Sample Number (IGSN) guide and template, with modifications to address Environmental Systems Science (ESS) sample needs and practicalities (IGSN-ESS). IGSNs are associated with standardized metadata to characterize a variety of different sample types (e.g. object type, material) and describe sample collection details (e.g. latitude, longitude, environmental context, date, collection method). Globally unique sample identifiers, particularly IGSNs, facilitate sample discovery, tracking, and reuse; they are especially useful when sample data is shared with collaborators, sent to different laboratories or user facilities for analyses, or distributed in different data files, datasets, and/or publications. To develop recommendations for multidisciplinary ecosystem and environmental sciences, we first conducted research on related sample standards and templates. We provide a comparison of existing sample reporting conventions, which includes mapping metadata elements across existing standards and Environment Ontology (ENVO) terms for sample object types and environmental materials. We worked with eight U.S. Department of Energy (DOE) funded projects, including those from Terrestrial Ecosystem Science and Subsurface Biogeochemical Research Scientific Focus Areas. Project scientists tested the process of registering samples for IGSNs and associated metadata in workflows for multidisciplinary ecosystem sciences. We provide modified IGSN metadata guidelines to account for needs of a variety of related biological and environmental samples. While generally following the IGSN core descriptive metadata schema, we provide recommendations for extending sample type terms, and connecting to related templates geared towards biodiversity (Darwin Core) and genomic (Minimum Information about any Sequence, MIxS) samples and specimens. ESS-DIVE recommends registering samples for IGSNs through SESAR, and we include instructions for registration using the IGSN-ESS guidelines. Our resulting sample reporting guidelines, template (IGSN-ESS), and identifier approach can be used by any researcher with sample data for ecosystem sciences.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Improvement of eukaryotic protein predictions from soil metagenomes

During the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI’s IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

NGEE Arctic Tram: Periodic Soil Moisture, Temperature, and Thaw Depth Measurements across Polygonal Tundra, Utqiagvik (Barrow), Alaska, 2014-2015

Manual measurements of soil moisture, temperature, and thaw depth were collected in the footprint of the NGEE Arctic Tram starting 2014-07-20 and continuing through 2015-07-16. There were 10 periodic sampling events with measurements in one *.csv file. These measurements were collected under the Tram observational platform. Probes were inserted into ground beneath the track closest to Tram sensors measurement locations at each Tram measurement position (Position # marked on the tracks). A MiniTrase Time Domain Reflectometry (TDR) instrument was used to measure volumetric water content (VWC; units = m3/m3). Soil temperature was measured with a thermocouple probe. Depth of thawed soil was measured from the top of the moss layer or top of soil. See user guide for more information *.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 OSTI2018

Copper and zinc levels in soil, water, wheat, and hair of inhabitants of three areas of the Orenburg region, Russia

Highlights: • Soil, water, wheat and hair levels of Zn and Cu in Orenburg region were studied. • Both Zn and Cu levels in the samples were higher in the eastern area. • Higher levels of Zn and Cu in the eastern area may occur due to industrial activities. • Water Zn levels were associated with hair Zn levels. The objective of the present study was to assess the level of zinc and copper in soil, water, wheat and hair of inhabitants of the western, central, and eastern areas of the Orenburg region. A total of 525 water, soil, and wheat samples, as well as 420 hair samples were assessed using atomic absorption spectrometry (water, soil, wheat) and inductively-coupled plasma mass spectrometry (hair). The highest levels of Zn and Cu in water (4.9(4.2–5.1) and 1.0(0.9–1.1) mg/l), soil (23.8(20.7–27.0) and 2.6(1.9–3.1) mg/kg), and wheat (24.7(20.5–31.0) and 4.8(4.2–5.5) mg/kg) were observed in the eastern area (p < 0.001). Hair zinc levels in inhabitants of the western (184(165–198) µg/g) and eastern (224(211–253) µg/g) areas of the region exceeded the respective values from the central area by 32% and 61% (p < 0.001). In turn, hair Cu levels in the central (16.4(14.3–17.8) µg/g) and eastern (17.9(16.4–19.0) µg/g) areas exceeded the values from the western area by 10% and 20%, respectively. Correlation analysis demonstrated that hair Zn levels were positively correlated with water and soil content, whereas wheat Zn levels were associated with soil and water content. For copper significant direct correlation was observed only between soil and water Cu content. In multiple regression models, only water zinc level was significantly associated with hair Zn content, although the general model accounted for 55% of variability of hair Zn content. Higher zinc and copper exposure in the eastern area is presumably associated with higher activity of metal-processing industry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes

Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait , a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.

Karaoz, Ulas↗
DOE OSTI2020

Mercury Methylation and Soil Organic Matter Degradation in Incubations with Added Acetate, Isotope-Labeled Mercury, and Selective Microbial Inhibitors, Teller and Council Sites, Seward Peninsula, 2018-2019

This dataset provides the results of laboratory soil microcosm incubation experiments conducted under anaerobic conditions with added acetate, isotope-labeled mercury, and selective microbial inhibitors (2-bromoethanesulfonate and sodium molybdate). The microcosms contained soil collected in August 2018 from the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) near Intensive Site 9 (TL_IS_9) and from the Council Road Site (CN_MM71). Incubations were conducted at 8°C for 180 days (Teller incubations) or 60 days (Council incubations). The microcosm headspace was sampled at designated intervals for greenhouse gas concentrations, then destructively harvested and extracted using ultrapure water and 0.1 M KCl for analysis of the porewater geochemistry. This dataset contains one pdf, two csv data files, and one zipped file with raw data.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 OSTI2025

An Evaluation of Actinide Reactivity with CO 2 , O 2 , and O 2 /He Gases using Inductively Coupled Plasma Tandem Mass Spectrometry: Application to Simultaneous Measurement of 241 Am/ 241 Pu Ratios in Unseparated Complex Matrices

Accurate actinide measurements are critical within the field of nuclear science. Traditional methods for actinide quantification require time-consuming sample processing prior to analysis. There is a need for rapid analytical techniques that still maintain a high degree of accuracy. In this work, actinide reactivity was assessed for multiple oxygen-containing reaction gases using quadrupole inductively coupled plasma tandem mass spectrometry (Q-ICP-MS/MS) to evaluate actinide analysis in complex sample matrices without analyte-matrix separation. A novel method was developed to measure 241 Am/ 241 Pu in complex sample matrices using O 2 /He reaction gas with no matrix removal or analyte pre-concentration. This inline method reduces matrix-derived polyatomic interferences that complicate traditional ICP-MS analyses by mass-shifting to 241 Am 16 O + and 241 Pu 16 O 2 + , allowing Am and Pu to be mass separated for simultaneous analysis. While mass shifting is efficient, a small portion of Am + (<1.3%) and Pu + (<1.4%) react to from AmO 2 + and PuO + , respectively. Therefore, a mass balance approach was used, in combination with reactivity determined from 242 Pu and 243 Am standard solutions, to correct for residual 241 PuO + and 241 AmO 2 + . The method was validated by measuring 241 Am/ 241 Pu in Pu isotope standards CRM-136 and CRM-137 (separated in March/April 1970 and February 2022, respectively) in both neat solutions and complex matrices containing diluted soil (NIST SRM 2711a, >1000 µg·g -1 ). Method detection limits of 15.9 and 9.6 fg·g -1 were determined for 241 Am and 241 Pu, respectively, and 241 Am/ 241 Pu ratios were measured with accuracies within <3.5%. In conclusion, this work presents the first direct analysis of 241 Am/ 241 Pu in unseparated complex matrices, advancing capabilities for rapid actinide measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Thorium, uranium and rare earth elements content in lanthanide concentrate (LC) and water leach purification (WLP) residue of Lynas advanced materials plant (LAMP)

Lynas Advanced Materials Plant (LAMP) has been licensed to produce the rare earths elements since early 2013 in Malaysia. LAMP processes lanthanide concentrate (LC) to extract rare earth elements and subsequently produce large volumes of water leach purification (WLP) residue containing naturally occurring radioactive material (NORM). This residue has been rising up the environmental issue because it was suspected to accumulate thorium with significant activity concentration and has been classified as radioactive residue. The aim of this study is to determine Th-232, U-238 and rare earth elements in lanthanide concentrate (LC) and water leach purification (WLP) residue collected from LAMP and to evaluate the potential radiological impacts of the WLP residue on the environment. Instrumental Neutron Activation Analysis and γ-spectrometry were used for determination of Th, U and rare earth elements concentrations. The results of this study found that the concentration of Th in LC was 1289.7 ± 129 ppm (5274.9 ± 527.6Bq/kg) whereas the Th and U concentrations in WLP were determined to be 1952.9±17.6 ppm (7987.4 ± 71.9 Bq/kg) and 17.2 ± 2.4 ppm respectively. The concentrations of Th and U in LC and WLP samples determined by γ- spectrometry were 1156 ppm (4728 ± 22 Bq/kg) and 18.8 ppm and 1763.2 ppm (7211.4 Bq/kg) and 29.97 ppm respectively. This study showed that thorium concentrations were higher in WLP compare to LC. This study also indicate that WLP residue has high radioactivity of {sup 232}Th compared to Malaysian soil natural background (63 - 110 Bq/kg) and come under preview of Act 304 and regulations. In LC, the Ce and Nd concentrations determined by INAA were 13.2 ± 0.6% and 4.7 ± 0.1% respectively whereas the concentrations of La, Ce, Nd and Sm in WLP were 0.36 ± 0.04%, 1.6%, 0.22% and 0.06% respectively. This result showed that some amount of rare earth had not been extracted and remained in the WLP and may be considered to be reextracted.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2021

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Abstract Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Results Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH 4 and CO 2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Conclusions Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Endophyte-Promoted Phosphorus Solubilization in Populus

Phosphorus is an important plant nutrient, but in soils the majority of phosphorus, present in the form of a phosphate, forms metal complexes in soil making it relatively unavailable to plants. Therefore, inorganic phosphate solubilization is an important process of plant growth promotion by plant associated bacteria and fungi. Non nodulating plant species have been shown to thrive in low-nutrient environments, in some instances by relying on plant associated microorganisms called endophytes. These microorganisms live within the plant and help supply nutrients for the plant. Despite their potential enormous environmental importance, there are a limited number of studies looking at the direct molecular impact of phosphate solubilizing endophytic bacteria on the host plant. In this work, we studied the impact of two endophyte strains of wild poplar (Populus trichocarpa) that solubilize phosphate. Using a combination of x-ray imaging, spectroscopy methods, and proteomics we report direct evidence of endophyte-promoted phosphorus uptake in poplar. We found that the solubilized phosphate inside the plant may react and become insoluble again suggesting that the phosphate could be re-released within the plant by endophytes. Using synchrotron x-ray fluorescence spectromicroscopy combined with x-ray absorption near-edge structure, we visualized the nutrient phosphorus inside poplar roots inoculated by the selected endophytes and found the phosphorus in both forms of organic and inorganic phosphates inside the root. Tomography-based root imaging revealed a markedly different root biomass and root architecture for poplar samples inoculated with the phosphate solubilizing bacteria strains. Proteomics characterization on poplar roots coupled with protein network analysis revealed novel proteins and metabolic pathways with possible involvement in endophyte enriched phosphorus uptake. These findings suggest an important role of endophytes for phosphorus acquisition and provide a deeper understanding of the critical symbiotic associations between poplar and the endophytic bacteria.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones

Global warming has shifted climate zones poleward or upward. Furthermore, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRI (Net Relatedness Index) values increased from 0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomybased association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-fortime substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Arbuscular mycorrhizal fungal community responses to drought and nitrogen fertilization in switchgrass stands

Anthropogenic global change is increasing the severity and frequency of abiotic stresses such as drought that are likely to affect soil communities. Arbuscular mycorrhizal fungi (AMF) play important roles in many soil processes, so it is important to understand how drought affects AMF biodiversity. This is especially relevant in agricultural systems where crops rely on AMF associations for water and nutrient uptake, and where management decisions such as crop selection and fertilizer application may influence how the AMF community responds to drought. In this study, we examined the effects of reduced precipitation and nitrogen fertilization on AMF richness, community composition, and root and soil colonization in monocultures of two cultivars of switchgrass (Panicum virgatum) grown for bioenergy feedstock. We conducted a two-year field experiment using rain-out shelters to manipulate precipitation in mature stands of switchgrass growing in a long-term nitrogen fertilization (0 or 56 kg N ha –1 ) experiment at the W.K. Kellogg Biological Station Long-Term Ecological Research site in Michigan, USA. We expected that AMF richness and colonization would decrease due to drought, as predicted by the stress exclusion hypothesis. Contrary to our expectations, we found that drought stress increased AMF species richness in fertilized plots by 15%; there was no effect of drought on AMF richness in unfertilized plots. Drought also significantly altered AMF community composition, primarily due to increases in Rhizophagus taxa abundance, and reduced AMF root colonization in switchgrass by 6%. We also found variation in AMF richness and colonization across switchgrass cultivars as well as sampling dates. Furthermore, the changes in AMF richness and composition that we observed in this study may have implications for perennial bioenergy feedstock selection and management as changes in AMF communities may feedback to affect host plants.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Site and endmember spectra of terrestrial vegetation and soils for the Colorado Headwaters Ecological Spectroscopy Study, June-July 2025

This dataset provides site and endmember spectra collected during the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS) campaign. The site spectra were collected to help validate airborne hyperspectral data acquired by the National Ecological Observatory Network's aerial observation platform (NEON AOP). Endmember spectra were collected to augment existing spectral libraries with additional samples of bare surfaces and non-photosynthetic vegetation. All measurements were acquired with an Analytical Spectral Devices (ASD) FieldSpec4 Hi-Res NG (Next Generation) spectroradiometer, which records radiance at 1nm (nanometer) intervals from the ultraviolet to the short-wave infrared (350-2500 nm). The dataset includes spectra measured at meadow sites where the CHESS team also collected vegetation samples for trait analyses. The site spectra were collected with the ASD FieldSpec4 palm grip attachment using an 8° field-of-view foreoptic. Site spectra are integrated measurements of the entire surface within the foreoptic’s field of view. For site-level spectra, the sun is the illumination source. A Spectralon panel mounted on a tripod was used for instrument optimization and white reference measurements for all site spectra. Site spectra were acquired within two hours of solar noon and within 48 hours of a NEON AOP overflight. Site spectra are labeled by date, sampling area, and site number according to the naming conventions of the CHESS campaign’s data management plan. The dataset also contains endmember spectra in the following categories: photosynthetic vegetation (PV), non-photosynthetic vegetation (NPV), bare (soil/rock), and flowers. Endmember measurements were acquired using either the contact probe or the leaf clip attachments of the ASD FieldSpec4. In these configurations, the bulb inside the spectrometer provides the light source for the measurements. The spectrometer was optimized and white reference measurements were recorded using the circular white pucks attached to the contact probe and leaf clip. Because they do not rely on solar illumination, contact probe and leaf clip measurements were collected during a broader time frame than the palm grip site spectra. Some endmembers were measured at CHESS meadow sites, while others were collected within the larger sampling area or in nearby locations (e.g. Gothic Townsite) with similar characteristics. Radiance, reflectance, and metadata files are split into three subfolders according to measurement type: proximal/palm grip (prx), contact probe (cp), and leaf clip (lc). Radiance spectra are provided in ASD file format (.asd file extension). All ASD files can be opened using the provided scripts. Metadata is provided in two formats: CSV file format (no geolocation) and GEOJSON file format (includes geolocation for each spectra). The dataset includes a set of pre-processed reflectance spectra as CSV files (yyyymmdd_rfl.csv). The python scripts and jupyter notebook used to calculate reflectance spectra from the ASD radiance data is included here and was previously published at: https://doi.org/10.3334/ORNLDAAC/2446. There is also a folder of JPEG photographs corresponding to selected spectra. We include a protocol document with detailed steps for ASD FieldSpec4 assembly and operations. This data additionally contains a file level metadata (flmd.csv) and data dictionary (dd.csv) file. Geospatial information: Geospatial data for mapping measurement site locations are in the files CHESS_polygons_lai_UTM.geojson, CHESS_polygons_shrub_UTM.geojson, and CHESS_polygons_meadow_UTM.geojson in the companion geospatial package for the 2025 CHESS campaign, ‘CHESS 2025: Location data for field observations and sampling’ (Henderson et al., 2026). CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgment: This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004) and was funded by EMIT Extended Mission Phase E Science.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2022

WHONDRS Surface Water Chemistry and Organic Matter Characterization along the St. Lawrence River's Inland to Coastal Gradient, Eastern North America (v2)

This dataset supports a broader study examining the inland (Lake Ontario) to coastal (North Atlantic Ocean) geochemistry gradient along the St. Lawrence River in Canada and the United States. The St. Lawrence River is unique in that it contains the convergence of multiple water masses with distinct water signatures that mix only slightly as the river flows downstream. The dataset provides dissolved organic carbon (DOC) and organic matter characterization data generated from surface water. Samples were collected by researchers on board the Lampsilis research vessel (l’Université du Québec à Trois-Rivières) and small boats (St. Lawrence River Institute of Environmental Sciences, Cornwall) at 94 locations across and along the St. Lawrence River to capture longitudinal and transverse variation. Related data were collected and will be published separately in collaboration with the MicrEAU Laboratory (François Guillemette; l’Université du Québec à Trois-Rivières) and the Exploration of Coastal Hydrobiogeochemistry Across a Network of Gradients and Experiments (EXCHANGE) program. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data (5) surface water sampling protocol; (6) readme; (7) methods codes; (8) international geo-sample number (IGSN) mapping file; and (9) folder of high resolution characterization of organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The FTICR folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. The data package was originally published in November 202. It was updated in April 2025 (v2; modified files). See the change history section in the readme for details.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Data from: "Warming of alpine tundra enhances belowground production and shifts community towards resource acquisition traits"

This archive contains data used to draw conclusions in “Warming of alpine tundra enhances belowground production and shifts community towards resource acquisition traits”, by Yang et al. 2020. Data were collected on Niwot Ridge, in an alpine meadow within the Alpine Treeline Warming Experiment (ATWE) field sites in Colorado, USA. Samples were also processed in the U.S. Geological Survey Forest and Rangeland Ecosystem Science Center, in Boise, Idaho. File formats in this archive include comma-separated values (.csv), portable document format (.pdf), Microsoft Excel (.xlsx), and two types of geospatial files: keyhole markup language (.kml), and ESRI shapefiles (.shp). Leaf scans are .jpg images, and root scans are .tiff/.tif images.The .csv files can be opened using R, Microsoft Excel, or any simple text-editing software such as TextEdit and Notepad. Microsoft Excel files can be opened using Microsoft Excel, and .pdf files can be opened with Adobe Acrobat Reader, Preview, or other compatible programs. Scanned images can be opened using any photo and/or picture viewing software.The .kml file can be opened using Google Earth and Google Maps, and the shapefiles can be opened by any programs compatible with shapefiles, such as the ArcGIS Desktop suite, and QGIS.------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Measures of belowground net primary productivity (BNPP) are required to understand whether aboveground net primary production (ANPP) changes reflect changes in allocation or are indicative of a whole plant NPP response. Plant functional traits provide a key way to scale from the individual plant to the community level, and provide insight into drivers of NPP responses to environmental change. We used infrared heaters to warm an alpine plant community at Niwot Ridge, Colorado, and applied supplemental water to compensate for soil water loss induced by warming. We measured ANPP, BNPP, and leaf and root functional traits across treatments after 5 years of continuous warming. Community-level ANPP and total NPP (ANPP + BNPP) did not respond to heating or watering, but BNPP increased in response to heating. Heating decreased community-level leaf dry matter content and increased total root length, indicating a shift in strategy from resource conservation to acquisition in response to warming.

13C/12C isotope ratio↗
DOE OSTI2014

Interactive Effects of Climate Change and Decomposer Communities on the Stabilization of Wood-Derived Carbon Pools: Catalyst for a New Study

Globally, forest soils store ~two-thirds as much carbon (C) as the atmosphere. Although wood makes up the majority of forest biomass, the importance of wood contributions to soil C pools is unknown. Even with recent advances in the mechanistic understanding of soil processes, integrative studies tracing C input pathways and biological fluxes within and from soils are lacking. Therefore, our research objectives were to assess the impact of different fungal decay pathways (i.e., white-rot versus brown-rot)—in interaction with wood quality, soil temperature, wood location (i.e., soil surface and buried in mineral soil), and soil texture—on the transformation of woody material into soil CO 2 efflux, dissolved organic carbon (DOC), and soil C pools. The use of 13 C-depleted woody biomass harvested from the Rhinelander, WI free-air carbon dioxide enrichment (Aspen-FACE) experiment affords the unique opportunity to distinguish the wood-derived C from other soil C fluxes and pools. We established 168 treatment plots across six field sites (three sand and three loam textured soil). Treatment plots consisted of full-factorial design with the following treatments: 1. Wood chips from elevated CO 2 , elevated CO 2 + O 3 , or ambient atmosphere AspenFACE treatments; 2. Inoculated with white rot (Bjerkandera adusta) or brown rot (Gloeophyllum sepiarium) pure fungal cultures, or the original suite of endemic microbial community on the logs; and 3. Buried (15cm in soil as a proxy for coarse roots) or surface applied wood chips. We also created a warming treatment using open-topped, passive warming chambers on a subset of the above treatments. Control plots with no added wood (“no chip control”) were incorporated into the research design. Soils were sampled for initial δ 13 C values, CN concentrations, and bulk density. A subset of plots were instrumented with lysimeters for sampling soil water and temperature data loggers for measuring soil temperatures. To determine the early pathways of decomposition, we measured soil surface CO 2 efflux, dissolved organic C (DOC), and DO 13 C approximately monthly over two growing seasons from a subsample of the research plots. To determine the portion of soil surface CO 2 efflux attributable to wood-derived C, we used Keeling plot techniques to estimate the associated δ 13 C values of the soil CO 2 efflux. We measured the δ 13 CO 2 once during the peak of each growing season. Initial values for soil δ 13 C values and CN concentrations averaged across the six sites were -26.8‰ (standard error = 0.04), 2.46% (se = 0.11), and 0.15% (se = 0.01), respectively. The labeled wood chips from the Aspen FACE treatments had an average δ13C value of -39.5‰ (se 0.10). The >12 ‰ isotopic difference between the soil and wood chip δ 13 C values provides the basis for tracking the wood-derived C through the early stages of decomposition and subsequent storage in the soil. Across our six research sites, average soil surface CO 2 efflux ranged from 1.04 to 2.00 g CO 2 m -2 h -1 for the first two growing seasons. No wood chip controls had an average soil surface CO 2 efflux of 0.67 g CO 2 m -2 h -1 or about half of that of the wood chip treatment plots. Wood-derived CO 2 efflux was higher for loam textured soils relative to sands (0.70 and 0.54 g CO 2 m -2 h -1 , respectively; p = 0.045)), for surface relative to buried wood chip treatments (0.92 and 0.39 g CO 2 m -2 h -1 , respectively; p < 0.001), for warmed relative to ambient temperature treatments (0.99 and 0.78 g CO 2 m -2 h -1 , respectively; 0.004), and for natural rot relative to brown and white rots (0.93, 0.82, and 0.78 g CO 2 m -2 h -1 , respectively; p = 0.068). Our first two growing seasons of soil surface CO 2 efflux data show that wood chip location (i.e., surface vs. buried chip application) is very important, with surface chips loosing twice the wood-derived CO 2 . The DOC data support this trend for greater loss of ecosystem C from surface chips. This has strong implications for the importance of root and buried wood for ecosystem C retention. This strong chip location effect on wood-derived C loss was significantly modified by soil texture, soil temperature, decomposer communities, and wood quality as effected by potential future CO 2 and O 3 levels.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Substantial and overlooked greenhouse gas emissions from deep Arctic lake sediment - supporting data and code

This data package contains data, descriptions, and code-based analyses that were used to support conclusions drawn in “Substantial and overlooked greenhouse gas emissions from deep Arctic lake sediment”, by Freitas et al. (2025) (https://doi.org/10.1038/s41561-024-01614-y). The study evaluated greenhouse gas production along a deep sediment core (20 m) taken in 2018 from below Goldstream Lake, a field site approximately 15 km north of Fairbanks, Alaska.The file “ESSDive_NFreitas_2024_flmd.csv” includes an overview of all other csv files in this data package, namely: sediment descriptions (depth and type of sediment), sediment characterizations (bulk density, gravimetric water content, total carbon, etc.), calculated respiration and temperature sensitivity values associated with year-long incubations of the sediment core, and the R code used to process the dataset. Additional details regarding the content of these files and how the calculations were performed are described in the Methods section of this archive. The “data_dictionary_ESSDive_NFreitas_2024_dd.csv” is a data dictionary for all files included in the data package. Each row in the data dictionary represents a column name in a given 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).Data package updates- August 2024: Title was updated, R code now includes a process for calculating potential production across the whole sediment column, the "sediment_column_production_potentials_ESSDive_NFreitas_2024.csv" is the associated data output file, and the file level metadata and data dictionaries were updated to reflect the contents of the additional csv file.- October 2024: Title was updated, and a statement was added to Step 2 of the Methods that describes that samples were collected (and exported) in a responsible manner and in accordance with relevant permits and local laws.- January 2025: Updated the associated manuscript details in the Abstract (manuscript title, publication date, DOI link) and in the Related References section (full citation).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Terrestrial Subsurface Ecosystem

The Earth’s crust is a solid cool layer that overlays the mantle, with a varying thickness of between 30-50 km on continental plates, and 5-10 km on oceanic plates. Continental crust is composed of a variety of igneous, metamorphic, and sedimentary rocks that weather and re-form over geologic cycles lasting millions to billions of years. At the crust surface, these weathered minerals and organic material combine to produce a variety of soils types that provide suitable habitats and niches for abundant microbial diversity (see Chapter 4). Beneath this soil zone is the subsurface. Once thought to be relatively free of microorganisms, recent estimates have calculated that between 1016-1017 g C biomass (2-19% of Earth’s total biomass) may be present in this environment (Whitman et al., 1998;McMahon and Parnell, 2014). Microbial life in the subsurface exists across a wide range of habitats: in pores associated with relatively shallow unconsolidated aquifer sediments to fractures in bedrock formations that are more than a kilometer deep, where extreme lithostatic pressures and temperatures are encountered. While these different environments contain varying physical and chemical conditions, the absence of light is a constant. Despite this, diverse physiologies and metabolisms enable microorganisms to harness energy and carbon for growth in water-filled pore spaces and fractures. Carbon and other element cycles are driven by microbial activity, which has implications for both natural processes and human activities in the subsurface, e.g., bacteria play key roles in both hydrocarbon formation and degradation. Hydrocarbons are a major focus for human utilization of the subsurface, via oil and gas extraction and potential geologic CO2 sequestration. The subsurface is also utilized or being considered for sequestered storage of high-level radioactive waste from nuclear power generation and residual waste from past production of weapons grade nuclear materials. While our understanding of the subsurface is continually improving, it is clear that only a small fraction of microbial habitats have been sampled and studied. In this chapter, we will discuss these studies in the context of the distribution of microbial life in the subsurface, the stresses that microorganisms must overcome to survive in these environments, and the metabolic strategies that are employed to harness energy in a region of the planet far-removed from sunlight. Finally, we will consider both beneficial and deleterious effects of microbial activity in the subsurface on human activities in this environment.

Wilkins, Michael J.↗