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DOE OSTI2022

The case for data science in experimental chemistry: examples and recommendations

The physical sciences community is increasingly taking advantage of the possibilities offered by modern data science to solve problems in experimental chemistry and potentially to change the way we design, conduct and understand results from experiments. Successfully exploiting these opportunities involves considerable challenges. In this Expert Recommendation, we focus on experimental co-design and its importance to experimental chemistry. We provide examples of how data science is changing the way we conduct experiments, and we outline opportunities for further integration of data science and experimental chemistry to advance these fields. Our recommendations include establishing stronger links between chemists and data scientists; developing chemistry-specific data science methods; integrating algorithms, software and hardware to ‘co-design’ chemistry experiments from inception; and combining diverse and disparate data sources into a data network for chemistry research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Transcriptomic data sets for Novosphingobium aromaticivorans grown with the β-5-linked aromatic dimer dehydrodiconiferyl alcohol and the related G-aromatic monomers vanillin and ferulic acid

ABSTRACT The transcriptomes of a 2-pyrone-4,6-dicarboxylic acid-producing strain of Novosphingobium aromaticivorans DSM12444 were determined when grown in minimal medium containing glucose alone or glucose plus vanillin, ferulic acid, or the β-5-linked aromatic dimer dehydrodiconiferyl alcohol as carbon sources. Here, we present the RNA-sequencing data we obtained.

Metz, Fletcher↗

DOE OSTI2024

Anticipating Optical Availability in Hybrid RF/FSO Links Using RF Beacons and Deep Learning

Radiofrequency (RF) communications offer reliable but low data rates and energy-inefficient satellite links, while free-space optical (FSO) promises high bandwidth but struggles with disturbances imposed by atmospheric effects. A hybrid RF/FSO architecture aims to achieve optimal reliability along with high data rates for space communications. Accurate prediction of dynamic ground-to-satellite FSO link availability is critical for routing decisions in low-earth orbit constellations. In this paper, we propose a system leveraging ubiquitous RF links to proactively forecast FSO link degradation prior to signal drops below threshold levels. This enables pre-calculation of rerouting to maximally maintain high data rate FSO links throughout the duration of weather effects. We implement a supervised learning model to anticipate FSO attenuation based on the analysis of RF patterns. Through the simulation of a dense lower earth orbit (LEO) satellite constellation, we demonstrate the efficacy of our approach in a simulated satellite network, highlighting the balance between predictive accuracy and prediction duration. An emulated cloud attenuation model is proposed to provide insight into the temporal profiles of RF signals and their correlation to FSO channel dynamics. Our investigation sheds light on the trade-offs between prediction horizon and accuracy arising from RF beacon numbers and proximity.

FSO availability↗

DOE OSTI2024

HERO WEC 2024 Hydraulic Configuration Deployment Data

The following submission includes raw and processed data from the in water deployment of NREL's Hydraulic and Electric Reverse Osmosis Wave Energy Converter (HERO WEC), in the form of parquet files, TDMS files, CSV files, bag files and MATLAB workspaces. This dataset was collected in March 2024 at the Jennette's pier test site in North Carolina. This submission includes the following: - Data description document (HERO WEC FY24 Hydraulic Deployment Data Descriptions.doc) - This document includes detailed descriptions of the type of data and how it was processed and/or calculated. - Processed MATLAB workspace - The processed data is provided in the form of a single MATLAB workspace containing data from the full deployment. This workspace contains data from all sensors down sampled to 10 Hz along with all array Value Added Products (VAPs). - MATLAB visualization scripts - The MATLAB workspaces can be visualized using the file "HERO_WEC_2024_Hydraulic_Config_Data_Viewer.m/mlx". The user simply needs to download the processed MATLAB workspaces, specify the desired start and end times and run this file. Both the .m and .mlx file format has been provided depending on the user's preference. - Summary Data - The fully processed data was used to create a summary data set with averages and important calculations performed on 30-minute intervals to align with the intervals of wave resource data reported from nearby CDIP ocean observing buoys located 20km East of Jennette's pier and 40km Northeast of Jennette's pier. The wave resource data provided in this data set is to be used for reference only due the difference in water depth and proximity to shore between the Jennette's pier test site and the locations of the ocean observing buoys. This data is provided in the Summary Data zip folder, which includes this data set in the form of a MATLAB workspace, parquet file, and excel spreadsheet. - Processed Parquet File - The processed data is provided in the form of a single parquet file containing data from all HERO WEC sensors collected during the full deployment. Data in these files has been down sampled to 10 Hz and all array VAPs are included. - Interim Filtered Data - Raw data from each sensor group partitioned into 30-minute parquet files. These files are outputs from an intermediate stage of data processing and contain the raw data with no Quality Control (QC) or calculations performed in a format that is easier to use than the raw data. - Raw Data - Raw, unprocessed data from this deployment can be found in the Raw Data zip folder. This data is provided in the form of TDMS, CSV, and bag files in the original format output by the MODAQ system. - Python Data Processing Script - This links to an NREL public github repository containing the python script used to go from raw data to fully processed parquet files. Additional documentation on how to use this script is included in the github repository. This data set has been developed by the National Renewable Energy Laboratory, operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. Funding provided by the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Water Power Technologies Office.

16 TIDAL AND WAVE POWER↗

DOE OSTI2023

Leaf Nitrogen and Carbon Content, and Leaf Mass Per Area, Kougarok Road, Seward Peninsula, Alaska, 2018

Nitrogen and carbon content, leaf mass per area (LMA) and leaf water content (LWC) of leaves sampled from locations on the Kougarok mile marker 64 NGEE Arctic site, Seward Peninsula, Alaska. Samples were collected in July 2018 from Alnus viridis, Betula nana, Betula glandulosa, Arctostaphylos alpina and Salix pulchra. This data package includes leaf sample information and trait data (*.csv). Metadata files include data descriptions (_dd.csv) for tabular data and a key to species symbols used in data files. All included files are listed and described in NGA207_flmd.csv. See data package NGA208 "Full spectrum 350-2500 nm canopy spectral reflectance, Seward Peninsula, Alaska, 2018" for linked canopy spectral reflectance data, dGPS locations and sample photographs. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

EGS Collab Experiment 1: Circulation Testing Processed data

This submission includes processed and reduced data for circulation testing that was conducted at the 164' fracture on the 4850 ft level of the Sanford Underground Research Facility. The circulation tests were done to test the flow through the 164' fracture in the EGS Collab Experiment 1 testbed on the 4850 ft level of the Sanford Underground Research Facility in order to validate computer models concerned with flow processes and heat exchange processes in EGS. This data was processed from raw data that is available in the GDR submission linked below: "EGS Collab Circulation Testing Raw Data and Documentation." Python scripts used to process and reduce the data are included. The scripts also serve as "documentation" as well as examples for data processing. More information about the test itself as well as the rationale and process of data processing is available at wiki page linked below.

15 GEOTHERMAL ENERGY↗

DOE OSTI2019

Full Integration of Lipidomics Data into Multi-OMIC Functional Enrichment

Lipids have numerous roles critical to living systems. Many of these vital functions are tightly linked or regulated by proteins. Even though the function of many lipid-related enzymes is known, direct links between most individual lipid species and the enzymes that metabolize them are severely lacking. This missing connection impedes biological progress. A resource that allows users to quickly identify protein-lipid relationships will advance our understanding of lipid homeostasis and metabolic perturbed systems. Databases are readily available for mapping small molecule metabolites (i.e., polar metabolites) and specific oxidized fatty acid lipids (e.g., arachidonic acid derivatives) to proteins/enzymes known to be directly involved in metabolism of these molecules (e.g. SMPDB, Reactome, HMDB, BioCyc). This enables the integration of metabolite and protein (as well as transcript) data when performing functional enrichment and metabolic modeling allowing researchers to rapidly examine metabolic pathways from multiple omics sources. Currently, linking lipidomics data with proteomics data is conducted using a time-intensive, user defined, manual process. Here we propose creating a tool that will link lipidomics and proteomics data and also conduct functional enrichment analysis and visualization allowing for full statistical integration. Using text-mining approaches, we will extract lipid references from uniprot and create a database linking lipid species to enzymes directly related to their metabolism. We will also extract directional annotation, which will allow even greater specificity when linking data types and will help eliminate false positives from functional associations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Appalachian Basin Play Fairway Analysis: Natural Sedimentary Reservoirs Data 2016 Revision

Tier 3 data for Appalachian Basin sectors of New York, Pennsylvania and West Virginia used in a Geothermal Play Fairway Analysis of opportunities for low-temperature direct-use applications of heat. It accompanies data and materials submitted as Geothermal Data Repository Submission "Natural Reservoir Analysis 2016 GPFA-AB" (linked below). Reservoir information are derived from oil and gas exploration and production data sets, or derived from those data based on further analysis. Data reported here encompass locations (horizontal and depth), geologic formation names, lithology, reservoir volume, porosity and permeability, and derived approximations of the quality of the reservoir. These differ from the linked 2015 data submission in that this file presents data for New York that are comparable to those in the other two states. In contrast, the 2015 data available measured differing attributes across the state boundaries.

15 GEOTHERMAL ENERGY↗

DOE OSTI2022

100 Gb/s High Throughput Serial Protocol (HTSP) for data acquisition systems with interleaved streaming

Demands on Field-Programmable Gate Array (FPGA) data transport have been increasing over the years as frame sizes and refresh rates increase. As the bandwidths requirements increase the ability to implement data transport protocol layers using "soft" programmable logic becomes harder and start to require harden IP blocks implementation. To reduce the number of physical links and interconnects, it is common for data acquisition systems to require interleaving of streams on the same link (e.g. streaming data and streaming register access). Further, this paper presents a way to leverage existing FPGA harden IP blocks to achieve a robust, low latency 100 Gb/s point-to-point link with minimal programmable logic overhead geared towards the needs of data acquisition systems with interleaved streaming requirements.

47 OTHER INSTRUMENTATION↗

DOE OSTI2019

Using the concordance of in vitro and in vivo data to evaluate extrapolation assumptions

Linking in vitro bioactivity and in vivo toxicity on a dose basis enables the use of highthroughput in vitro assays as an alternative to traditional animal studies. In this study, we evaluated assumptions in the use of a high-throughput, physiologically based toxicokinetic (PBTK) model to relate in vitro bioactivity and rat in vivo toxicity data. The fraction unbound in plasma (fup) and intrinsic hepatic clearance (Clint) were measured for rats (for 67 and 77 chemicals, respectively), combined with fup and Clint literature data for 97 chemicals, and incorporated in the PBTK model. Of these chemicals, 84 had corresponding in vitro ToxCast bioactivity data and in vivo toxicity data. For each possible comparison of in vitro and in vivo endpoint, the concordance between the in vivo and in vitro data was evaluated by a regression analysis. For a base set of assumptions, the PBTK results were more frequently better associated than either the results from a “random” model parameterization or direct comparison of the “untransformed” values of AC50 and dose (performed best in 51%, 28%, and 21% of cases, respectively). We also investigated several assumptions in the application of PBTK for IVIVE, including clearance and internal dose selection. One of the better assumptions sets–restrictive clearance and comparing free in vivo venous plasma concentration with free in vitro concentration–outperformed the random and untransformed results in 71% of the in vitro-in vivo endpoint comparisons. These results demonstrate that applying PBTK improves our ability to observe the association between in vitro bioactivity and in vivo toxicity data in general. This suggests that potency values from in vitro screening should be transformed using in vitro-in vivo extrapolation (IVIVE) to build potentially better machine learning and other statistical models for predicting in vivo toxicity in humans

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Epidemiologic Study of One Million U.S. Radiation Workers and Veterans

The single most important question in radiation epidemiology is determining the level of health risks associated with radiation exposures that occur gradually over time. The study of one million early U.S. radiation workers and veterans has been designed to provide information on risk following chronic exposures by focusing on occupational groups with differing radiation exposure patterns, including intakes of radionuclides. The cost-efficient study builds on the investments made and foundations laid by investigators and government agencies over the past 30-40 years, which have established early worker cohorts that can now provide answers to questions on the lifetime human health risks associated with low-level radiation exposures. Within the overall goal of the epidemiologic study of one million U.S. radiation workers and veterans, this project had a total of nine specific aims which included studies of six populations for multiple endpoints including cancer overall mortality, leukemia and non-cancer mortality. The six populations included: Mound, Ohio, workers exposed to polonium, tritium and plutonium; nuclear power plant workers within the Landauer dosimetry and Nuclear Regulatory Commission data files; industrial radiographers; Mallinckrodt uranium workers; uranium workers who linked with the US Renal Data System; and nuclear weapons test participants. Over 400,000 workers and atomic veterans are included in these populations, with vital status being determined and analyses of all causes of death undertaken. A critical, integral component of the studies has been comprehensive evaluations of dosimetry involving, in many cases, complex dose reconstructions, and assessments of uncertainties. The work has also involved development of state-of-the art statistical approaches and modeling. All nine aims were accomplished successfully, resulting in publication of two NCRP documents, 13 literature papers, numerous Boice Reports in Health Physics News and many presentations of the work at scientific meetings. Furthermore, recommendations have been developed for an approach to integrate epidemiologic observations with radiation biology for risk assessment and biological models of radiation effect. The results of this project, as well as ongoing epidemiology studies of US radiation workers and veterans, are providing much-needed insights into complex issues regarding cancer and non-cancer health risks from low dose irradiation, how to apply a "dose and dose rate effectiveness factor" to scale the risks from the A-bomb survivor data to current occupational and environmental circumstances, and how to evaluate risk following intakes of radioactive substances. In addition to application to radiation workers, the results of the studies can provide guidance as society debates the role of nuclear energy and deals with nuclear waste, threats of terrorist attacks with nuclear/radiological devices, the remarkable increase in medical exposures to CT scans and nuclear imaging, and to NASA as radiation protection for astronauts on long-duration mission beyond low-Earth orbit is planned.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2016

Uncertainty Evaluation of Measurements with Pyranometers and Pyrheliometers

Evaluating photovoltaic (PV) cells, modules, arrays and systems performance of solar energy relies on accurate measurement of the available solar radiation resources. Solar radiation resources are measured using radiometers such as pyranometers (global horizontal irradiance) and pyrheliometers (direct normal irradiance). The accuracy of solar radiation data measured by radiometers depends not only on the specification of the instrument but also on a) the calibration procedure, b) the measurement conditions and maintenance, and c) the environmental conditions. Therefore, statements about the overall measurement uncertainty can only be made on an individual basis, taking all relevant factors into account. This paper provides guidelines and recommended procedures for estimating the uncertainty in measurements by radiometers using the Guide to the Expression of Uncertainty (GUM) Method. Special attention is paid to the concept of data availability and its link to uncertainty evaluation.

14 SOLAR ENERGY↗

DOE OSTI2014

THE NEW ONLINE METADATA EDITOR FOR GENERATING STRUCTURED METADATA

Nobody is better suited to “describe” data than the scientist who created it. This “description” about a data is called Metadata. In general terms, Metadata represents the who, what, when, where, why and how of the dataset [1]. eXtensible Markup Language (XML) is the preferred output format for metadata, as it makes it portable and, more importantly, suitable for system discoverability. The newly developed ORNL Metadata Editor (OME) is a Web-based tool that allows users to create and maintain XML files containing key information, or metadata, about the research. Metadata include information about the specific projects, parameters, time periods, and locations associated with the data. Such information helps put the research findings in context. In addition, the metadata produced using OME will allow other researchers to find these data via Metadata clearinghouses like Mercury [2][4]. OME is part of ORNL’s Mercury software fleet [2][3]. It was jointly developed to support projects funded by the United States Geological Survey (USGS), U.S. Department of Energy (DOE), National Aeronautics and Space Administration (NASA) and National Oceanic and Atmospheric Administration (NOAA). OME’s architecture provides a customizable interface to support project-specific requirements. Using this new architecture, the ORNL team developed OME instances for USGS’s Core Science Analytics, Synthesis, and Libraries (CSAS&L), DOE’s Next Generation Ecosystem Experiments (NGEE) and Atmospheric Radiation Measurement (ARM) Program, and the international Surface Ocean Carbon Dioxide ATlas (SOCAT).Researchers simply use the ORNL Metadata Editor to enter relevant metadata into a Web-based form. From the information on the form, the Metadata Editor can create an XML file on the server that the editor is installed or to the user’s personal computer. Researchers can also use the ORNL Metadata Editor to modify existing XML metadata files.As an example, an NGEE Arctic scientist use OME to register their datasets to the NGEE data archive and allows the NGEE archive to publish these datasets via a data search portal (http://ngee.ornl.gov/data). These highly descriptive metadata created using OME allows the Archive to enable advanced data search options using keyword, geo-spatial, temporal and ontology filters. Similarly, ARM OME allows scientists or principal investigators (PIs) to submit their data products to the ARM data archive.How would OME help Big Data Centers like the Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC)?The ORNL DAAC is one of NASA’s Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project. The ORNL DAAC archives data produced by NASA's Terrestrial Ecology Program. The DAAC provides data and information relevant to biogeochemical dynamics, ecological data, and environmental processes, critical for understanding the dynamics relating to the biological, geological, and chemical components of the Earth's environment. Typically data produced, archived and analyzed is at a scale of multiple petabytes, which makes the discoverability of the data very challenging. Without proper metadata associated with the data, it is difficult to find the data you are looking for and equally difficult to use and understand the data.OME will allow data centers like the NGEE and ORNL DAAC to produce meaningful, high quality, standards-based, descriptive information about their data products in-turn helping with the data discoverability and interoperability. Useful Links:USGS OME: http://mercury.ornl.gov/OME/NGEE OME: http://ngee-arctic.ornl.gov/ngeemetadata/ARM OME: http://archive2.ornl.gov/armome/Contact: Ranjeet Devarakonda (devarakondar@ornl.gov)References:[1] Federal Geographic Data Committee. Content standard for digital geospatial metadata. Federal Geographic Data Committee, 1998.[2] Devarakonda, Ranjeet, et al. "Mercury: reusable metadata management, data discovery and access system." Earth Science Informatics 3.1-2 (2010): 87-94.[3] Wilson, B. E., Palanisamy, G., Devarakonda, R., Rhyne, B. T., Lindsley, C., & Green, J. (2010). Mercury Toolset for Spatiotemporal Metadata.[4] Pouchard, L. C., Branstetter, M. L., Cook, R. B., Devarakonda, R., Green, J., Palanisamy, G., ... & Noy, N. F. (2013). A Linked Science investigation: enhancing climate change data discovery with semantic technologies. Earth science informatics, 6(3), 175-185.

FGDC CSDGM↗

DOE OSTI2026

A ModEx Framework for Watershed Subsurface Investigation With Limited Geophysical Data Using Machine Learning and Hydrologic Modeling

Abstract Subsurface heterogeneity influences watershed hydrology strongly but remains difficult to characterize at catchment scales with sparse and costly field data. Geophysical surveys such as electromagnetic induction (EMI) provide local spatial subsurface images yet scaling them to watershed scales and converting EMI‐derived resistivity into hydraulic properties remains a challenge. We present a Model–Experiment (ModEx) framework that integrates limited EMI data with machine learning (ML) and hydrologic modeling to improve process representation and guide field investigations. Sparse EMI surveys were scaled to the catchment scale using a Random Forest model, and the resulting resistivity fields were combined with nearby borehole constraints to parameterize a hydrologic model. The EMI‐informed hydrological simulations improved predictions of streamflow sustained by subsurface flow and shallow saturation patterns. By combining EMI data and ML with hydrologic modeling, the ModEx framework guides future subsurface surveys, providing a transferable and efficient strategy for data–model integration across diverse watersheds. Plain Language Summary Mapping the underground network of soil and rock that controls water is essential for predicting floods and droughts, but seeing underground is difficult and expensive. We cannot drill everywhere, so scientists use geophysical tools to scan broad areas. There are two key challenges: these geophysical scans are often sparse across the whole watershed, and the geophysical data is hard to translate into water‐related properties. We used artificial intelligence to solve these problems. We taught a computer to find patterns linking the limited geophysical data to the land surface properties. This allowed it to fill in the gaps and create a complete, useful subsurface map for the entire watershed. This new map improves hydrologic simulations, leading to more accurate predictions of water movement in the watershed. It also helps scientists build better models with less data and generates a priority map showing where to measure next, making future investigations more efficient. Key Points Limited EMI scaled with ML improves catchment‐scale subsurface parameterization for hydrologic models The framework integrates hydrologic modeling with limited geophysical data to support subsurface investigation design ModEx framework offers a transferable data–model integration strategy that quantifies and reduces uncertainty guiding watershed studies

Chen, Hang↗

DOE OSTI2019

Radiation-Hardened, High-Speed Parallel VCSEL Links for High-Energy Physics

Vega Wave Systems, Inc. has been awarded a Small Business Innovative Research (SBIR) Phase II proposal to the U.S. Department of Energy entitled “Radiation-Hardened, High-Speed Parallel VCSEL Links For High-Energy Physics.” The technology proposed under this program is a significant advance (up to 4x) in data rate over current optical link technologies under development. Fermilab supports the technology developed under this proposal as a radiation-hardened, cost-effective solution for optical links for the high-speed data communications in High-Energy Physics and agrees to provide consulting and test engineering in support of this program. Fermilab staff will provide consulting services along with high speed testing of modules before and after radiation testing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Fusing time-varying mosquito data and continuous mosquito population dynamics models

Climate change is arguably one of the most pressing issues affecting the world today and requires the fusion of disparate data streams to accurately model its impacts. Mosquito populations respond to temperature and precipitation in a nonlinear way, making predicting climate impacts on mosquito-borne diseases an ongoing challenge. Data-driven approaches for accurately modeling mosquito populations are needed for predicting mosquito-borne disease risk under climate change scenarios. Many current models for disease transmission are continuous and autonomous, while mosquito data is discrete and varies both within and between seasons. This study uses an optimization framework to fit a non-autonomous logistic model with periodic net growth rate and carrying capacity parameters for 15 years of daily mosquito time-series data from the Greater Toronto Area of Canada. The resulting parameters accurately capture the inter-annual and intra-seasonal variability of mosquito populations within a single geographic region, and a variance-based sensitivity analysis highlights the influence each parameter has on the peak magnitude and timing of the mosquito season. This method can easily extend to other geographic regions and be integrated into a larger disease transmission model. This method addresses the ongoing challenges of data and model fusion by serving as a link between discrete time-series data and continuous differential equations for mosquito-borne epidemiology models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Root genetics in the field to understand drought adaptation and carbon sequestration (Final Scientific/Technical Report)

For all crop plants, roots play a critical role in growth. Roots anchor the plants, and are the primary site of nutrient and water uptake. Roots are also the main source of C to soil in the form of root tissues and exudates, and thus greatly influence SOM stocks. To perform these functions, primary roots extend into soil, producing a network of branching roots of characteristic form, known as its root system architecture (RSA). RSA varies among species, and among varieties within a species that are adapted to different environments. Root traits are major targets for the second green revolution because of their potential to improve crop productivity, increase drought tolerance and nutrient acquisition, and increase C capture of soil. Improving the quality of roots in maize will be particularly valuable, since this crop is planted on over 92 million acres annually in the US. The future sustainability of agricultural systems relies on their ability to enhance soil organic matter (SOM) storage and reduce GHG emissions, while maintaining or enhancing productivity. This program had two components, Sensors and Models. For the first component, we designed and built a high-throughput phenotyping platform for root pulling of maize plants. This eliminated the physical labor of manually pulling up plants and reduced the number of personnel required down to one. The standardized pulling mechanism allowed recording force curves during the pulling process, providing additional information. We validated that the maximum force for pulling the root system was well-correlated with the root system mass and provided root crowns for further RSA analysis. These root crowns identified significant correlations with 2D root area and root depth, along with 3D root volume, total root length and number of root tips. We then used this system for field-based studies in maize on the genetics of root system architecture and its relation to nitrogen-use efficiency (NUE), including using lines relevant to the Corteva breeding program. Varieties were also evaluated at Corteva sites in the cornbelt and Danforth farm in Missouri, to establish responses across sites. From these studies we have identified genetic loci associated with root traits and created mutant lines for these loci and correlations of root traits with NUE. For the Models component, we worked to incorporate root and soil characteristics into the MEMS 2.0 soil and ecosystem biogeochemical model. Existing soil C models, such as Century, are unable to represent specific root trait interactions with the soil environment and therefore to accurately forecast the potential C sequestration benefits of root breeding under different climatic and soil type conditions. We have developed the MEMS 2.0 ecosystem biogeochemical model to improve quantification of farm-scale soil carbon and greenhouse gas emissions. The new knowledge and large datasets produced by this project will be used to develop and drive an innovative model capable of forecasting the impacts on soil C stocks and nutrient dynamics. An innovation was to use the empirical data from the field studies (in 1, above) to model genetic variation in nitrogen use efficiencies and soil C input. Our work demonstrated that maize root-derived C rapidly replaces existing soil C and after 3 years of continuous maize, up to 20% of soil organic C in the topsoil (0-15cm) and 3% in the subsoil (15-30cm) was contributed by maize. However, this contribution did not entirely represent a net increase. Root C contribution to soil was affected by maize genetics. We have analyzed soils derived from the CSU field trials for C and N stocks, in the different soil physical fractions represented by the MEMS model, using both physical fractionation with elemental analyses, and Fourier transformed infrared spectroscopy. Data will be used to link crop nitrogen use efficiencies with soil C sequestration and provide data to bridge the field trials with the model development, for verification of model predictions. The project had a number of successful outcomes: we have used the new phenotyping platform to identify new genetic loci that can enhance root phenotypes; we have partnered with multiple maize seed companies phenotype varieties in their breeding programs; we have developed the MEMS model that can help inform industry on the potential for carbon sequestration in the agricultural sector, and which is now available at the CSU Soil Carbon Solutions Center for use.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

RB-TnSeq barcode abundance data sets for Novosphingobium aromaticivorans grown on the β-5-linked aromatic dimer dehydrodiconiferyl alcohol

ABSTRACT A randomly barcoded transposon insertion sequencing (RB-TnSeq) library of Novosphingobium aromaticivorans DSM12444 was grown in media containing either glucose or the β-5-linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) as the sole carbon source. The cultures were grown to saturation and then sequenced, yielding the barcode abundance data sets presented here.

Metz, Fletcher↗