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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↗

Analysis of Respirator Cartridge Performance Testing on the 702-AZ Primary Exhauster for the Hanford AY/AZ Tank Farms during a Waste-Disturbing Event

Washington River Protection Solutions (WRPS) conducted tests using two types of chemical cartridges for use in air-purifying respirators (APR) to determine the period of time that the cartridges would provide adequate performance1 for APRs used to protect workers when exposed to a mixture of Chemicals of Potential Concern (COPC) from vapors exiting the 702-AZ Primary Exhauster for the Hanford AY-AZ tank farms. Unlike prior cartridge testing on the 702-AZ Primary Exhauster, the recent tests were performed during a waste-disturbing event. The Occupational Safety and Health Administration (OSHA) identifies cartridge testing as a valid approach for establishing a cartridge change schedules. Testing is commonly applied in situations where mixtures of COPCs exist, and where other approaches, such as manufacturer recommendations and modeling, are less reliable. The tests were designed and conducted to assure measurement and/or control of the key variables OSHA identified as important to estimate the cartridge service life, including temperature, humidity, COPC concentration, breathing rate, and cartridge adsorption capacity. Testing was conducted from February 10–11, 2017, on a slipstream from the 702-AZ exhauster fed to a respirator cartridge test stand developed by WRPS in collaboration with HiLine Engineering (Richland, Washington). Multipurpose respirator cartridges, SCOTT 7422-SD1 and SCOTT 7422-SC1 (SCOTT Safety, Monroe, North Carolina), were assessed on separate days. Sample media (sorbent tubes) and canisters (e.g., Summa) sampling were used to collect samples of the vapor stream entering and exiting the respirator cartridge and were subsequently analyzed for COPC concentrations. Pacific Northwest National Laboratory was tasked with conducting an independent analysis of the analytical results and making recommendations based on the results for respiratory cartridge performance and service life.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Trinity 78th Anniversary: re-discovered and newly edited unclassified footage shows use of tanks to collect radioactive samples immediately after Trinity test (Rev. 1)

On July 16, 1945, at 5:29 a.m., a team of Los Alamos scientists successfully detonated the world’s first atomic bomb at a remote section of south-central New Mexico desert, then known as the Alamogordo Bombing Range. This full-scale test, dubbed “Trinity” by the Lab’s first Director J. Robert Oppenheimer, proved the viability of the implosion-type bomb known as The Gadget and ushered in the Atomic Age. Three weeks after Trinity, two Los-Alamos created atomic weapons – Little Boy and Fat Man – were released above Japan, helping to end World War II and changing the course of history forever.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Williston Basin Carbon Ore, Rare Earth, and Critical Minerals (CORE-CM) Program

The U.S. Department of Energy’s (DOE’s) Office of Fossil Energy awarded 13 Carbon Ore, Rare-Earth and Critical Minerals (CORE-CM) programs as part of the CORE-CM Initiative, designed to develop the technology and upstream and midstream supply chains to extract rare-earth elements (REEs) and CMs from the nation’s coal supplies. The intent is to catalyze regional economic growth and job creation while strengthening the use of domestic resources. The Williston Basin CORE-CM Program aims to drive the expansion and transformation of coal and coal-based resource usage within the Williston Basin to produce REEs, CMs, and nonfuel carbon-based products (CBPs). The work constitutes Phase 1 of a long-term program. The objectives of Phase 1 are to identify the existing knowledge base and gaps and to develop a series of assessments/plans, including an initial basinal assessment; a characterization and data acquisition plan; a waste stream reuse plan; a basinal strategies assessment for infrastructure, industries, and business; a technology assessment, development, and field-testing plan; a technology innovation center plan(s); and a stakeholder outreach and education plan. Originally, the CORE-CM programs were to do little if any sample collection as part of the Phase 1 program. As part of the ongoing interactions with DOE regarding the progress of the 13 CORE-CM programs, DOE has decided to extend Phase 1 with additional funding to allow all of the Phase 1 CORE-CM programs to collect and characterize more samples that have potential to be sources of REEs and CMs. The goal of this project is to initiate the development of a new industry in the resource-rich Williston Basin that will generate economic growth and job creation through a coalition team of private industry; university; and state, local, and federal government entities. A coalition team of nearly 30 private industry; university; and state, local, and federal government partners was formed for this program. Partners include the University of North Dakota Energy & Environmental Research Center, Institute for Energy Studies, and Nistler College; North Dakota State University; Montana Tech University; Pacific Northwest National Laboratory; Critical Materials Institute; North Dakota Geological Survey; South Dakota Geological Survey; U.S. Geological Survey; North American Coal Corporation; BNI Energy; Basin Electric Power Cooperative; Minnkota Power Cooperative; and many more.

Kay, John P.↗

Surface Water Chemistry and Water and Nitrogen Isotopes, Teller Road Site, Seward Peninsula, Alaska, 2016 and 2017

Data include results from water chemistry and water isotope analyses for surface water samples collected at the NGEE Arctic Teller Road site at mile marker 27 (TL_MM27) on the Seward Peninsula, Alaska, July through September of 2016 and May through September of 2017. The samples were collected using automated samplers (ISCO Model 6712; Teledyne, USA), with regular collection (every 24 hrs in 2016 and every 48 hrs in 2017). Surface water samples were collected from three locations along the main drainage: ISCO 1 from the tributary (64.729060°, -165.946210°), ISCO 3 which was located upstream (64.733640°, -165.955410°) and ISCO 2 which was located downstream (64.726410°, -165.946820°). Dataset includes a *.pdf user guide and one *.csv data file.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 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↗

Trepanning Graphite Samples at a Shutdown Magnox Reactor: A US-UK Joint Exercise for Nuclear Verification

In April 2022, a team sponsored by the US DOE Office of Nuclear Verification (ONV) shipped trepanning equipment to the nuclear power station at Trawsfynydd, Wales, UK to collect samples from the graphite moderator of Reactor 1. The sampling campaign to collect 48 graphite samples was completed in five weeks beginning July 11. Half the samples will be analyzed in the US to determine the total energy production of the facility. The other half will be analyzed by Magnox Ltd. to support decisions for options for the ultimate decommissioning path for the facility. This paper provides a description of the equipment and the operations required to trepan, collect, and package the samples while controlling the small amounts of radioactive graphite dust entrained on and within the tool. The most important sample parameter needed is the precise location of the sample, to within ±6 mm in a fuel channel, while the tool is deployed to between 12 and 20 meters below the operations floor; our means of achieving this precision is given.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

SPRUCE Precipitation Chemistry and Bulk Atmospheric Deposition Beginning in 2013

This data set reports the chemistry of precipitation water that was collected at the SPRUCE site located in the S1 bog and calculated values of bulk atmospheric deposition of solutes in precipitation. Sample collection and analyses started during December of 2013 and will continue for the duration of the experiment. Precipitation samples were collected year round on an event-basis from up to three individual collectors. Samples were either composited or individually analyzed, depending on the total volume of water available relative to the amount needed to complete all laboratory analyses. Funnel/bottle collectors were used to collect rainfall and buckets were used to collect snowfall and mixed precipitation. Samples were analyzed for pH, specific conductivity, nutrient concentrations (ammonium, nitrate, soluble reactive phosphorus, total nitrogen), cation concentrations (calcium, magnesium), anion concentrations (chloride, sulfate), total organic carbon concentrations, and natural-abundance stable isotopes of water (δ18O-H2O and δD-H2O). Bulk deposition was calculated by multiplying rainfall amount by solute concentration for ammonium, nitrate, soluble reactive phosphorus (SRP), total nitrogen, calcium, magnesium, chloride, sulfate, and total organic carbon. All measurements were made at the 8.1-ha S1 bog forest site in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF).

54 ENVIRONMENTAL SCIENCES↗

Genome-resolved metagenomics and metatranscriptomics of microbial communities in three meander-bound floodplain soils along the East River, Colorado.

This dataset comprises paired environmental and genomic data for soil samples collected across meander-bound floodplains G (ERMG), L (ERML) and Z (ERMZ). A total of 96 soil samples (32 per floodplain) from the ~ 10-25 cm layer were collected in September 2015, during base flow conditions. An additional 32 soil samples were collected from ERML in September 2016, including three samples from a depth just above the water table. A subset of samples (14) collected in 2016 were used for metatranscriptomics as well as metagenomics. The data package includes: 1) A spread sheet with sample names, location and depth by meander-bound floodplain. 2) Total organic carbon (TOC), total inorganic carbon (TIC), total carbon (TC = TOC + TIC), total nitrogen (TN), and the TOC to TN ratio (TOC:N) from 2015 subsamples. 3) Soil chemistry for 2016 subsamples. 4) A spread sheet with elevation, Easting, Northing, and topographic position index (TPI) for each site sampled in 2015. 5) A kml file, which can be viewed in Google Earth, with the locations of the 96 soil sampling sites along the East River Watershed Floodplain in Colorado. Metagenomics and metatranscriptomics data, as well as reconstructed genomes, are available elsewhere (see data package methods and bioRxiv preprint for links to the data). 6) Two sets of reconstructed genomes with overlapping members (see bioRxiv preprint for description and associated data). Metagenomes and metatranscriptomes are available elsewhere (see data package methods and bioRxiv preprint). To view tar.gz files, the following software can be used: https://www.gnu.org/software/tar/, https://www.7-zip.org/.

54 ENVIRONMENTAL SCIENCES↗

R&D Outcomes of Surrogate Environmental Swipe Manufacturing Technique Method Development for Arms Control and Treaty Verification Applications

The analysis of environmental samples is a critical component of nuclear compliance verification and safeguards activities. While the associated particle analyses have benefitted from recent advances in the production of actinide-bearing particulates with uniform and well-characterized particle size, material phase, and isotopic ratios to serve as reference materials for calibration and interlaboratory comparisons, there is an outstanding need for surrogate environmental samples, which resemble field-collected samples, with the aforementioned reference particulates to support future nuclear compliance verification exercises and method development. This effort seeks to leverage the recent advances in tailored reference particle production to generate surrogate environmental swipe samples via parallel production techniques (direct and indirect) which are uniquely suited to the hydrothermal and aerosol-based synthesis routes developed at PNNL and SRNL, respectively. PNNL’s hydrothermal particle production method was used to generate surrogate reference particles for the indirect production of test swipes.

54 ENVIRONMENTAL SCIENCES↗

NW-BRaVE T3 Hydroplane Project Close: Project Close-out for T3 Hydroplane Analysis

Thrust 3 of the Northwest Biopreparedness Research in a Virtual Environment was an expansive project including method development, sample collection and sequence analysis. The sampling occurred over a multi-year period to generate metagenomic datasets that inform cyanophage-picocyanobacterial interactions in the Salish Sea across a moderate timeframe and geographical range. Part of the thrust’s aim was to validate how much experimental structural and multiomics work in a model organism (Prochlorococcus Marinus, str. MED4) from thrusts 1 and 2 would carry over into a broader range of related organisms in the natural world, to address a fundamental question in scientific preparation for epidemics: whether and how much experimental information from known and experimentally tractable species can translate to actionable biological information in unknown species. In other words, thrust 3 aimed to find out whether the model organism experiments matter in terms of how organisms interact. This report updates work described in Johnson and Pollock 2025 (1).

54 ENVIRONMENTAL SCIENCES↗

Indigenous Organic Molecular Biosignatures are Detectable via ToF-SIMS of a Kerogen-rich Jurassic Clay

Time of Flight - Secondary Ion Mass Spectrometry (ToF-SIMS) is a Mass Spectrometry (MS) imaging technique that can be used in conjunction with traditional organic geochemical analysis (organics extracted from a crushed sample) in order to determine how molecules observed in the organic extracts were incorporated into a particular rock sample. This type of analysis may be used on samples collected as part of Mars Sample Return (MSR) in order to determine if potential organic compounds were indigenous to Mars or whether they are contaminants.Here we show that Organic Molecular Biosignatures (OMBs including steranes and derivatives of a carotenoid) are detectable via ToF-SIMS within a Jurassic mudstone. The OMBs are only detectable in areas with high organic carbon, likely kerogen, indicating that they are indigenous to the rock. We conclude that: I) Indigenous OMBs are detectable via ToF-SIMS in ancient, kerogen-rich samples; II) the presence of a molecular ion strengthens the interpretation of ToF-SIMS spectra of complex natural material, and III) the spatial co-occurrence of kerogen and potentially indigenous OMBs in ancient sediments is a valid test of their character. These conclusions are directly relevant to MSR sample selection as well as the analysis of MSR samples upon return.

Pasterski, Michael↗

Soil physical and thermal properties from soil samples at multiple locations at Teller Road Site, Seward Peninsula, Alaska, 2019

This dataset contains results of the laboratory analysis of soil samples collected across the watershed located at miles #27 along the Teller road, near Nome, AK. The dataset includes 124 soil samples retrieved from 52 locations during the first week of August 2019. The soil samples were collected in the top 1.2 m of soil with volume known samples, analyzed with a thermal analyser to infer thermal parameters (thermal conductivity, volumetric heat capacity and thermal diffusivity), and then processed in a lab for estimation of their bulk density, water content, carbon and nitrogen content, soil texture, and elemental fractions. This dataset has one csv file and one pdf file.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

SPRUCE Peat Mercury, Methylmercury and Sulfur Concentrations from Experimental Plot Cores, Beginning in 2014

This data set reports the results of physical and chemical analyses of peat core samples from the SPRUCE experimental study plots located in the S1-Bog in northern Minnesota, 40 km north of Grand Rapids in the USDA Forest Service Marcell Experimental Forest (MEF). Sample collection and analyses started in June of 2014 and will continue for the duration of the experiment. Core samples are collected annually from all 12 plots to a depth of 200cm in 10cm and 25cm increments. Samples are analyzed for total mercury concentration, methylmercury concentration, percent carbon, percent nitrogen, and percent sulfur.

54 ENVIRONMENTAL SCIENCES↗

SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA’s GenomeTrakr network

ABSTRACT Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA‘s genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject,PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA’s GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA. IMPORTANCE This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA’s laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.

Microbiology↗

Lead isotopic compositions of airborne particulates collected from snow and from dry deposition in the East River Watershed, Colorado and at the Southern Sierra Critical Zone Observatory, California

The data set consists of lead (Pb) isotopic ratios (206Pb/207Pb and 208Pb/207Pb, as well as 206Pb/204Pb, 207Pb/204Pb, 208Pb/204Pb) for particulate samples collected from snow and dry deposition. This was part of a study (O’Day et al. 2020) that was looking at the speciation of phosphorous in splits of these samples to evaluate the flux and bio-availability of phosphorous to the mountain sites in the study. The Pb isotopic data allow sourcing of long-range transported Pb, specifically the fraction of Pb sourced in Asia, and so a comparison of the relative distances of PM sources between the high and low elevation sites. Samples were collected at the East River Watershed, CO (dry deposition collected over Sept.-Oct. 2016, show sampling winter 2017) and at the Southern Sierra Critical Zone Observatory (dry deposition collected over Sept-Nov 2016, July-Sept 2017, June-July 2017). The data includes Pb concentration data, as well as calculated fraction of the Pb sourced in Asia. This data set was published in part in O’Day et al. (2020) Phosphorus Speciation in Atmospherically Deposited Particulate Matter and Implications for Terrestrial Ecosystem Productivity. ES&T, https://dx.doi.org/10.1021/acs.est.9b06150

54 ENVIRONMENTAL SCIENCES↗

Ice nucleating particle concentrations in the Arctic during MOSAiC 2020

This data set contains ice nucleating particle (INP) measurements, using Colorado State University’s (CSU) Ice Spectrometer (IS) of samples collected during the Multidisciplinary Drifting Observatory for the Study of Arctic Climate (MOSAiC) field campaign. Samples were collected from five different media: aerosol filters, meltwater, ice cores, snow pits, and bulk sea water (BSW).

54 ENVIRONMENTAL SCIENCES↗

Porewater and Surface Water Chemistry of Wetland, Old Woman Creek National Estuarine Research Reserve, Huron, OH, 2022-07-06 to 2023-12-15

This dataset contains the chemistry data of surface water and porewater samples collected from a wetland, referred to as The Cove, at Old Woman Creek Estuarine Research Reserve in Huron, OH. Surface and pore water samples were taken to analyze what nutrient and/or metal constituents were present at different depths in the wetland at different times and to compare to redox potential values. Porewater was collected by constructed sippers and deployed into the underlying soil of the wetland, and they were samples approximately every 2 weeks (when groundwater was present) in 2023. Surface water was collected approximately 1 inch below the surface of the water column (if available) via a syringe. Unfiltered and 0.45 micron filtered samples were collected. Samples were analyzed for various chemistry and is reported in the SWChem (surface water chemistry) and PWChem (porewater chemistry) .csv datafiles. Collection information about the samples can be found within the PWChem_SWChem_SampleMetdata.csv file. All files associated with this dataset are listed in the PWChem_SWChem_FLMD.csv file.

54 ENVIRONMENTAL SCIENCES↗

Solute chemistry for streams draining geomorphic features and varying land cover gradients in the East River watershed, Colorado

This dataset contains solute chemistry data and GPS coordinates for surface water samples collected in the East River watershed in the Elk and West Elk Ranges of Colorado from August 3rd through August 11th, 2022. Samples were collected from streams and groundwater seeps as part of a comprehensive analysis within the watershed of how different geomorphic features (such as landslides and rock glaciers) along with variations in land cover (such as the presence of vegetation) affect stream water quality in this Rocky Mountain headwater environment. This dataset includes concentrations of the following in a single csv file: fluoride, chloride, sulfate, nitrate, calcium, potassium, magnesium, sodium, silicon, and total organic carbon (TOC). All concentrations are reported in mg/L. The sulfate data in this version have been updated to account for an earlier ion chromatograph instrument method error whereby sulfate and bromide peaks overlapped in calibration solution samples, biasing calculated sulfate concentrations low by 30-50%. Sulfate data reported herein are from a re-run of the samples performed in December 2024 using a corrected instrument method. All samples were stored under refrigerated conditions and filtered on initial collection.

54 ENVIRONMENTAL SCIENCES↗