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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Terrestrial laser scanning data (Levels 0 and 1) from Urban Biogeochemistry Pilot Project sites, Knoxville, Tennessee, Jul 2024 - Jul 2025

This data package contains data from terrestrial laser scanning (TLS) at five urban park sites in Knoxville, Tennessee, USA. All parks include open-grown and/or closed-canopy trees and mixed nearby land use. These study sites were established as part of the Urban Biogeochemistry Pilot Project, which has an overall goal of better understanding how hydrobiogeochemical cycling is altered within the human environment. These five sites represent a gradient of urbanization, and were instrumented to understand hydrological and biogeochemical cycling (e.g., soil moisture, soil physical properties and biogeochemistry, tree transpiration, species type). The TLS data archived here were collected to provide detailed, three-dimensional information about forest structure. Specifically, data were collected to allow tree- and stand-level characterization of woody structure and leaf area. TLS scans were placed to capture the area around trees with sap flow sensors, and as much of a 50 m radius area around the meteorological station as possible given site property limits. Derived products will allow upscaling of water content and transpiration data. This data package contains the following data: - High-level files document further details of the campaign and data package: 1_CampaignSummary.csv provides details about the campaign and study site, 2_ScanAreasDetail.csv provides details about each separate scan area (groups of scans post-processed into a single point cloud), 3_TerrestrialLidarSensor.csv provides further technical details about the Riegl VZ-400i TLS sensor, TLS_CSV_dd.csv is a CSV Data Dictionary providing information about the fields in CSV files following the ESS-DIVE CSV File Formatting Guidelines Reporting Format, TLS_flmd.csv is a File Level Metadata file providing information about each file in the data package following the ESS-DIVE File Level Metadata Reporting Format, and README.txt is a text file describing the overall project and file structure. - Level 0 data are the raw data (.PROJ folders) as recorded by the Riegl VZ-400i TLS instrument before scan co-registration and post-processing with the Riegl's proprietary RiSCAN PRO software, which requires a license. - Level 1 data contain post-processed, co-registered data from each scan area. The "PointClouds" folder for each scan area contains a .las file with 1 cm resolution point cloud data exported from RiSCAN PRO. These are the main files likely to be of interest to most users and can be further processed with any software capable of manipulating .las files (e.g. Python, R CloudCompare). The "Project Information" folder contains log files from post-processing in RiSCAN PRO that may be of interest to users who want to see detailed records of post-processing, including all PDF reports generated by RiSCAN PRO. The "ScanPositions" folder contains information about the final position of all TLS scans, after post-processing, in multiple formats. The file ScanPositions_*.csv provides final geo-referenced scan positions, and the file SOP_backup_*.csv can be used in RiSCAN PRO to restore the co-registered scan positions if users wish to re-process raw data (Level 0 .PROJ folders) with RiSCAN PRO software (e.g., subsample to a different resolution, exclude a certain scan position, or apply different filters on reflectance or deviation values) without redoing time-consuming co-registration steps.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Biogeochemistry of Pond B (Savannah River Site, South Carolina, USA): Sediment Core, Total extraction data, Pond B Savannah River Site July 2019. Subsurface Biogeochemistry of Actinides SFA

Pond B at Savannah River Site (SRS, South Carolina) is a monomictic reservoir that received SRS R reactor cooling water from 1961–1964. Previous studies conducted between the 1980s–1990s on the water column and sediments of Pond B measured trace amounts of Pu (33 MBq 238Pu and 430 MBq 239,240Pu), 241Am, and 137Cs. Since then, the pond has been relatively isolated and the radionuclide concentrations have not been monitored over time. Herein, about 30 years after the last publication on Pond B, we are re-evaluating the geochemistry and radionuclide distribution within Pond B at four locations along a horizontal transect from the inlet to outlet.This study investigated the distribution of anthropogenic radionuclides Pu-239 and Cs-137 along with total organic carbon, iron, and trace element in contaminated sediments of Pond B at the Savannah River Site (SRS). Pond B received reactor cooling water from 1961 to 1964, and trace amounts of Pu-239 and Cs-137 during operations. Our study collected sediment cores to determine concentrations of Pu-239, Cs-137, and major and minor elements in solid phase, pore water and an electrochemical method was used on wet cores to determine dissolved elemental concentrations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Fire, dust, air and water: Improving aerosol biogeochemistry interactions in ACME. Final report

Aerosol-biogeochemistry interactions will have important consequences for human health, ecosystem services, and climate feedbacks over the next several decades. In this proposal we seek to link how human activities on land, including direct industrial emissions and landscape fires, impact the atmosphere and the biogeochemistry of the ocean and land. Our overall goal was to complement existing work at DOE labs to improve the capability and performance of the E3SM model in short-term, high-resolution projections of climate. Projections of ocean uptake of anthropogenic carbon are highly dependent on the details of the ocean physical and biogeochemistry parameterizations. Potentially equally important are the estimates of increases in iron and soluble nitrogen deposition in aerosols to the open ocean, but there are substantial uncertainties in these feedbacks. The E3SM land model simulates natural and anthropogenic fires, but improvement is needed to more accurately simulate fire responses to climate variability as well as fire contributions to terrestrial climate feedbacks. This proposal addressed four of the six priorities within the ACME/E3SM call by improving the representation of fire, industrial combustion sources, and desert dust and adding iron and soluble iron to the atmospheric chemistry (1). Our work focused on improving ocean biogeochemistry and the response of the oceans to anthropogenic atmospheric iron and nitrogen (3). We also improved the representation of land disturbance on fires and fire mediated carbon cycle feedbacks in the land model (4). Finally we had planned to couple the land, atmosphere and ocean biogeochemical systems (6) and explore how this coupling changes the feedbacks in the climate system. Our work under this proposal was separated into the following 5 tasks: i) improve representation of fire dynamics in both boreal and tropical ecosystems, ii) improve estimates of industrial emissions of iron and phosphorus, iii) improve representation of atmospheric iron, phosphorus and nitrogen transport, chemistry and deposition, iv) improve representation of iron, phosphorus and nitrogen deposition impacts on ocean biogeochemistry, and v) couple emissions into atmosphere, to deposition onto land and ocean biogeochemistry. For all 5 tasks, we conducted offline experiments of the historical period to enable comparison with available aerosol and land surface observations. We had planned to conduct fully coupled simulations, however, these will be conducted as part of the coupling in version 3 and 4 of the E3SM model, and thus have not been completed.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2020

Tracking Improvement in Simulated Marine Biogeochemistry Between CMIP5 and CMIP6

Purpose of Review The changes or updates in ocean biogeochemistry component have been mapped between CMIP5 and CMIP6 model versions, and an assessment made of how far these have led to improvements in the simulated mean state of marine biogeochemical models within the current generation of Earth system models (ESMs). Recent Findings The representation of marine biogeochemistry has progressed within the current generation of Earth system models. However, it remains difficult to identify which model updates are responsible for a given improvement. In addition, the full potential of marine biogeochemistry in terms of Earth system interactions and climate feedback remains poorly examined in the current generation of Earth system models. Summary Increasing availability of ocean biogeochemical data, as well as an improved understanding of the underlying processes, allows advances in the marine biogeochemical components of the current generation of ESMs. The present study scrutinizes the extent to which marine biogeochemistry components of ESMs have progressed between the 5th and the 6th phases of the Coupled Model Intercomparison Project (CMIP).

Marine Biogeochemistry↗
DOE OSTI2020

Tracking Improvement in Simulated Marine Biogeochemistry Between CMIP5 and CMIP6

The changes or updates in ocean biogeochemistry component have been mapped between CMIP5 and CMIP6 model versions, and an assessment made of how far these have led to improvements in the simulated mean state of marine biogeochemical models within the current generation of Earth system models (ESMs). The representation of marine biogeochemistry has progressed within the current generation of Earth system models. However, it remains difficult to identify which model updates are responsible for a given improvement. In addition, the full potential of marine biogeochemistry in terms of Earth system interactions and climate feedback remains poorly examined in the current generation of Earth system models. Increasing availability of ocean biogeochemical data, as well as an improved understanding of the underlying processes, allows advances in the marine biogeochemical components of the current generation of ESMs. The present study scrutinizes the extent to which marine biogeochemistry components of ESMs have progressed between the 5th and the 6th phases of the Coupled Model Intercomparison Project (CMIP).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

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

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

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2022

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

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

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

BioGeoChemistry at Interfaces (LLNL SFA OBER FY21 Program Management and Performance Report)

The focus of the BioGeoChemistry at Interfaces (formerly BioGeoChemistry of Actinides) SFA is to identify and quantify the biogeochemical processes and the underlying mechanisms that control actinide mobility in an effort to reliably predict and control the cycling and migration of actinides in the environment. The research approach includes: (1) Field Studies (Research Thrust 1) that capture actinide behavior on the timescale of decades and (2) Fundamental Laboratory Studies (Research Thrust 2) that isolate specific biogeochemical processes observed in the field. These Research Thrusts are underpinned by the unique capabilities and staff expertise at Lawrence Livermore National Laboratory, allowing the BioGeoChemistry at Interfaces SFA to advance our understanding of actinide migration behavior in the environment, and serve as an international resource for environmental radiochemistry research (Figure 1).

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2022

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

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

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

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

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

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2010

The Sensitivity of Simulated Ocean Biogeochemistry to Forcing Fields Derived from NCEP and MERRA Reanalysis Products

Ocean biogeochemistry models are typically forced by atmospheric and oceanic data derived from reanalysis products. For the NASA Ocean Biogeochemistry Model (NOBM) such reanalysis forcing fields include: surface wind stress, sea surface temperature, ice distributions, shortwave radiation, surface wind speeds and surface atmospheric pressure. Additionally, proper computation of ocean irradiance requires reanalysis products of relative humidity and precipitable water (in addition to aerosol and cloud information which is derived from satellite data). The question posed here is, does the choice of reanalysis products make a difference in the representation of ocean biology and biogeochemistry? NOBM was forced by NCEP and MERRA reanalysis products for the period 2002-2009. We find that in 2009 global distributions and abundances of biological variables (total chlorophyll and nutrients) and carbon (dissolved inorganic and organic carbon and surface pCO2) were similar between the two different forcing fields. Global statistical comparisons with satellite and in situ data also showed negligible differences.

Gregg, Watson↗
DOE OSTI2021

Improving Marine Biogeochemistry-Climate Feedbacks in ACME (Final Report)

Improve representation of marine biogeochemistry within E3SM to better capture climate-biogeochemistry feedbacks. This overall goal includes a number of components listed below. A key goal of this project is to better simulate the biological carbon pump, the transfer of carbon from surface waters to the ocean interior by sinking particulate organic matter (POM) and transport of dissolved organic matter (DOM). This is a primary feedback to climate as it directly modifies the air-sea CO 2 flux.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Biogeochemistry of the Antrim Shale Natural Gas Reservoir

The Antrim Shale, located in the Michigan Basin, United States (U.S.), is a major U.S. shale play having produced over 2.5 Trillion Cubic Feet (Tcf) of unconventional shale natural gas as of 2010. The shallow nature of this formation sets it apart from other, more characterized unconventional shale gas plays. The depth of gas production of the Antrim ranges from approximately 150 to 600 m and it is typically vertically drilled, contrary to deeper, horizontally drilled shales. A thorough understanding of the biogeochemistry and microbiology of this complex system will be advantageous for improving well performance, produced water management, and potential biocidal treatment as microbial community composition can vary substantially even among closely spaced wells. In this study, we analyzed produced water collected from nine different wells in the Antrim Shale by investigating the geochemical and microbial community composition of the produced water to gain greater insight into the overall biogeochemistry of this unique shale system. The majority of the wells from this study had high total dissolved solids (TDS) primarily composed of chloride and sodium, averaging 86,804 mg/L with a maximum 116,223 mg/L; however, three of the wells sampled along the northern margin of the basin exhibited significantly lower TDS ranging from 4932 to 6496 mg/L. Overall, our microbial community analysis revealed relatively low abundance within our samples and high variability of the microbial community among the sampled wells. The majority of bacterial sequences were identified within Proteobacteria, Firmicutes, and Actinobacteria phyla and metagenomic sequencing revealed the low presence of Methanobacteriaceae within each sample. We also investigated potential microbial community drivers and found that TDS, sodium, chloride, iodide, bromide, ammonium, potassium, and strontium were significantly correlated with the observed microbial community. The varying geochemical conditions between wells demonstrate different subsurface environmental niches, potentially driving the heterogeneous microbial communities we observed from well to well. This analysis suggests an important relationship between both well location and geochemistry and the observed microbial community that can persist in the reservoir. Continued studies of the Antrim Shale will improve our understanding of the complex interdependencies of this ecosystem.

03 NATURAL GAS↗
DOE OSTI2024

Influence of open ocean biogeochemistry on aerosol and clouds: Recent findings and perspectives

Aerosols and clouds are key components of the marine atmosphere, impacting the Earth’s radiative budget with a net cooling effect over the industrial era that counterbalances greenhouse gas warming, yet with an uncertain amplitude. Here we report recent advances in our understanding of how open ocean aerosol sources are modulated by ocean biogeochemistry and how they, in turn, shape cloud coverage and properties. We organize these findings in successive steps from ocean biogeochemical processes to particle formation by nucleation and sea spray emissions, further particle growth by condensation of gases, the potential to act as cloud condensation nuclei or ice nucleating particles, and finally, their effects on cloud formation, optical properties, and life cycle. We discuss how these processes may be impacted in a warming climate and the potential for ocean biogeochemistry—climate feedbacks through aerosols and clouds.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Analytical and Computational Advances, Opportunities, and Challenges in Marine Organic Biogeochemistry in an Era of “Omics”

Advances in sampling tools, analytical methods, and data handling capabilities have been fundamental to the growth of marine organic biogeochemistry over the past four decades. There has always been a strong feedback between analytical advances and scientific advances. However, whereas advances in analytical technology were often the driving force that made possible progress in elucidating the sources and fate of organic matter in the ocean in the first decades of marine organic biogeochemistry, today process-based scientific questions should drive analytical developments. Several paradigm shifts and challenges for the future are related to the intersection between analytical progress and scientific evolution. Untargeted “molecular headhunting” for its own sake is now being subsumed into process-driven targeted investigations that ask new questions and thus require new analytical capabilities. However, there are still major gaps in characterizing the chemical composition and biochemical behavior of macromolecules, as well as in generating reference standards for relevant types of organic matter. Field-based measurements are now routinely complemented by controlled laboratory experiments and in situ rate measurements of key biogeochemical processes. And finally, the multidisciplinary investigations that are becoming more common generate large and diverse datasets, requiring innovative computational tools to integrate often disparate data sets, including better global coverage and mapping. Here, we compile examples of developments in analytical methods that have enabled transformative scientific advances since 2004, and we project some challenges and opportunities in the near future. We believe that addressing these challenges and capitalizing on these opportunities will ensure continued progress in understanding the cycling of organic carbon in the ocean.

59 BASIC BIOLOGICAL SCIENCES↗