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Boye, Kristin

Publications and source records attributed to Boye, Kristin.

At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Simulation of anoxic lenses as exporters of reactivity in alluvial aquifer sediments

Sedimentary interfaces between contrasting hydrogeological facies in alluvial aquifers drive the development of biogeochemical interfaces that influence subsurface and surface water quality. Here, we calibrate a reactive transport model on a series of dual-domain column experiments, where centimeter-scale, low-permeability, organic-rich anoxic lenses are embedded in coarser-grained aquifer material. Simulations explicitly account for C, Fe, and S cycling at the interface between the lenses and the aquifer in water-saturated conditions. Our results highlight the role of fine-grained, organic-rich inclusions not only as sources or sinks for redox-sensitive species, but also as exporters of nutrients that stimulate downgradient biogeochemical cycling. By releasing large amounts of organic carbon into the surrounding aquifer, such lenses drive the development of proximal secondary reduction zones ("halos"), characterized by high microbial activity (e.g., sulfate reduction) and accumulation of reduced reaction products (e.g., iron sulfide). If similar secondary reduction zones develop within the hydraulically conductive domain of an aquifer, they would be highly susceptible to changes in hydrologic conditions, for instance oxygen pulses associated with seasonal snowmelt. Furthermore, our results also emphasize the limitations of relying solely on aqueous species measurements to inform reactivity in systems where fast redox cycling and/or sizeable particulate transport may limit the signature of reactivity in the dissolved phase.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Sulfur Biogeochemical Cycling and Redox Dynamics in a Shale-Dominated Mountainous Watershed

Sulfur (S) is an essential macronutrient and important component of the earth’s crust, and its cycling has critical impacts on trace metal mobility, water quality, and human health. Pyrite weathering is the primary pathway by which sulfur enters surface waters. However, biogeochemical cycling of sulfur in soils and the river corridor mediates sulfate exports. In this study, we identified the major forms of sulfur across multiple compartments and scales in a pristine mountainous watershed, including shale bedrock weathering profiles, hillslope soils, and alluvial floodplain sediments, in order to provide insight into biogeochemical sulfur cycling in a hydrologically variable alpine system. X-ray absorption near-edge spectroscopy (XANES) analysis of shale weathering profiles showed clear evidence of pyrite oxidation to sulfate, with large accumulations of intermediate S(0) (20%–53%). Micro-scale XANES showed evidence of reprecipitation of pyrite at fracture surfaces within the permanently saturated zone. Organic sulfur dominated S speciation in shallow hillslope soil and floodplain sediment, with little evidence of reduced inorganic S. However, mackinawite formation, representing active sulfate reduction, was observed in saturated oxbow sediments and saturated weathered shale underlying floodplain sediments. Further evidence of sulfate reduction from aqueous sulfur isotopic analysis was observed in shallow groundwater transects across an Fe-reducing meander, whereas increases in pore water sulfate concentrations implied sulfur oxidation at other locations. Furthermore, the data present an integrated picture of sulfur cycling in a shale-dominated watershed, where riverine sulfate exports are mediated by biological cycling, particularly in redox-stratified and temporally dynamic hyporheic zone sediments.

58 GEOSCIENCES↗
DOE OSTI2022

ESS-DIVE Reporting Format for Sample-based Water and Soil Chemistry Measurements

The ESS-DIVE (Environmental Systems Science Data Infrastructure for a Virtual Ecosystem) reporting format for sample-based water and soil chemistry measurements are written guidelines and spreadsheet templates, that facilitate archiving water/soil/sediment chemistry data. The templates and terminology lists provided as part of the reporting format can help organize data and potentially enable data reuse.The reporting format consists of a general instructions file (instructions.md) as well as more detailed instructions files for each template (files beginning “Detailed_Instructions_*.md). The “examples” folder includes an example of each data template with just the limited set of required fields filled out as well as other examples with both required and optional fields complete.The 'templates' folder contains CSV templates for data, methods, and terminology file templates. Similar to the examples folder, the blank templates are provided with versions for required fields only as well as required and optional fields. Lastly, the term list folder provides common terminology used in each of the templates as well as a definition and any constraints for the fields.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Data from: “Enabling FAIR data in Earth and environmental science with community-centric (meta)data reporting formats”

This dataset contains supplementary information for a manuscript describing the ESS-DIVE (Environmental Systems Science Data Infrastructure for a Virtual Ecosystem) data repository's community data and metadata reporting formats. The purpose of creating the ESS-DIVE reporting formats was to provide guidelines for formatting some of the diverse data types that can be found in the ESS-DIVE repository. The 6 teams of community partners who developed the reporting formats included scientists and engineers from across the Department of Energy National Lab network. Additionally, during the development process, 247 individuals representing 128 institutions provided input on the formats. The primary files in this dataset are 10 data and metadata crosswalk for ESS-DIVE’s reporting formats (all files ending in _crosswalk.csv). The crosswalks compare elements used in each of the reporting formats to other related standards and data resources (e.g., repositories, datasets, data systems). This dataset also contains additional files recommended by ESS-DIVE’s file-level metadata reporting format. Each data file has an associated dictionary (files ending in _dd.csv) which provide a brief description of each standard or data resource consulted in the data reporting format development process. The flmd.csv file describes each file contained within the dataset.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Greenhouse production contributes to pesticide occurrences in Swedish streams

Greenhouse and other covered cultivation systems have increased globally over the past several decades, leading to considerably improved product quality and productivity per land area unit. However, there is a paucity in information regarding the environmental impacts of covered production systems, especially regarding pesticides entering the surrounding environment. Aiming to address this knowledge gap, we collected grab samples downstream of greenhouses from seven Swedish streams every 14 days during a 12 month period. In three of the streams, samples were also taken upstream of the greenhouses and in four of the streams time-integrated samples were collected by TIMFIE samplers in the period between grab sampling occasions. The samples were analyzed for 28 substances (27 that were permitted for use in greenhouse production systems in Sweden and one degradation product to a permitted substance). Pesticide use journals were collected from the greenhouse producers for the 12 month period. The results were examined for indications of greenhouse contributions to detection frequencies, maximum and average concentrations, and potential ecotoxicicity in several ways: (1) comparing locations downstream of greenhouses with registered use of a substance with those without registered use, (2) comparing results from this study with those from the Swedish environmental monitoring program of pesticides in surface water from catchments with no greenhouses from the same period and region, (3) comparing concentration trends with registered pesticide application times in the greenhouses, and (4) comparing up- and downstream concentrations. The results strongly suggest that greenhouse applications do contribute to pesticide occurrences, maximum and median concentrations for most of the pesticides included in this study, and to potential toxicity to aquatic organisms for several of them, most notably imidacloprid, acetamiprid, carbendazim, and pirimicarb.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics

Abstract The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Organic compounds alter the preference and rates of heavy metal adsorption on ferrihydrite

The availability of heavy metals in terrestrial environments is largely controlled by their interactions with minerals and organic matter, with iron minerals having a particularly strong role in heavy metal fate. Because soil organic matter contains a variety of compounds that differ in their chemical properties, the underlying impact organic matter-soil mineral associations bestow on heavy metal binding is still unresolved. Here, we systematically examine the binding of Cd, Zn and Ni by a suite of organic-ferrihydrite assemblages, chosen to account for various compound chemistries within soil organic matter. We posited that organic compound functionality would dictate the extent of association with the organic-ferrihydrite assemblages. Increased heavy metal binding to the assemblages was observed and attributed to the introduction of additional binding sites by the organic functional groups with differing metal affinities. Furthermore, the relative increase depended on the metal's Lewis acidity and followed the order Cd > Zn > Ni, whereas the reverse order was obtained for metal binding by pristine ferrihydrite (Ni > Zn > Cd). Citric acid-, aspartic acid- and cysteine-ferrihydrite assemblages also enhanced the metal binding rate. X-ray absorption spectroscopy revealed that the organic coating contributed significantly to Zn binding by the assemblages, despite relatively low organic surface coverage. Our findings provide valuable information on the nature of heavy metal-organic-mineral interactions and metal adsorption processes regulating their bioavailability and transport.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A Guide to Using GitHub for Developing and Versioning Data Standards and Reporting Formats

Abstract Data standardization combined with descriptive metadata facilitate data reuse, which is the ultimate goal of the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. Community data or metadata standards are increasingly created through an approach that emphasizes collaboration between various stakeholders. Such an approach requires platforms for collaboration on the development process that centers on sharing information and receiving feedback. Our objective in this study was to conduct a systematic review to identify data standards and reporting formats that use version control for developing data standards and to summarize common practices, particularly in earth and environmental sciences. Out of 108 data standards and reporting formats identified in our review, 32 used GitHub as the version control platform, and no other platforms were used. We found no universally accepted methodology for developing and publishing data standards. Many GitHub repositories did not use key features that could help developers to gather user feedback, or to create and revise standards that build on previous work. We provide guidance for community‐driven standard development and associated documentation on GitHub based on a systematic review of existing practices.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Sample Identifiers and Metadata to Support Data Management and Reuse in Multidisciplinary Ecosystem Sciences

Physical samples are foundational entities for research across biological, Earth, and environmental sciences. Data generated from sample-based analyses are not only the basis of individual studies, but can also be integrated with other data to answer new and broader-scale questions. Ecosystem studies increasingly rely on multidisciplinary team-science to study climate and environmental changes. While there are widely adopted conventions within certain domains to describe sample data, these have gaps when applied in a multidisciplinary context. In this study, we reviewed existing practices for identifying, characterizing, and linking related environmental samples. We then tested practicalities of assigning persistent identifiers to samples, with standardized metadata, in a pilot field test involving eight United States Department of Energy projects. Participants collected a variety of sample types, with analyses conducted across multiple facilities. We address terminology gaps for multidisciplinary research and make recommendations for assigning identifiers and metadata that supports sample tracking, integration, and reuse. Furthermore, our goal is to provide a practical approach to sample management, geared towards ecosystem scientists who contribute and reuse sample data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Simulated Aquifer Heterogeneity Leads to Enhanced Attenuation and Multiple Retention Processes of Zinc

Alluvial aquifers serve as one of the main water sources for domestic, agricultural, and industrial purposes globally. Groundwater quality, however, can be threatened by naturally occurring and anthropogenic metal contaminants. Differing hydrologic and biogeochemical conditions between predominantly coarse-grained aquifer sediments and embedded layers or lenses of fine-grained materials lead to variation in metal behavior. Here, we examine processes controlling Zn partitioning within a dual-pore domain-reconstructed alluvial aquifer. Natural coarse aquifer sediments from the Wind River-Little Wind River floodplain near Riverton, WY, were used in columns with or without fine-grained lenses to examine biogeochemical controls on Zn concentrations, retention mechanisms, and transport. Furthermore, following the introduction of Zn to the groundwater source, Zn preferentially accumulated in the fine-grained lenses, despite their small volumetric contributions. While the clay fraction dominated Zn retention in the sandy aquifer, the lenses supported additional reaction pathways of retention—the reducing conditions within the lenses resulted in ZnS precipitation, overriding the contribution of organic matter. Zinc concentration in the groundwater controlled the formation of Zn-clays and Zn-layered double hydroxides, whereas the extent of sulfide production controlled precipitation of ZnS. Our findings illustrate how both spatial and compositional heterogeneities govern the extent and mechanisms of Zn retention in intricate groundwater systems, with implications for plume behavior and groundwater quality.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Templates for developing and versioning data standards and reporting formats using GitHub

This data package contains three templates that can be used for creating README files and Issue Templates, written in the markdown language, that support community-led data reporting formats. We created these templates based on the results of a systematic review (see related references) that explored how groups developing data standard documentation use the Version Control platform GitHub, to collaborate on supporting documents. Based on our review of 32 GitHub repositories, we make recommendations for the content of README Files (e.g., provide a user license, indicate how users can contribute) and so 'README_template.md' includes headings for each section. The two issue templates we include ('issue_template_for_all_other_changes.md' and 'issue_template_for_documentation_change.md') can be used in a GitHub repository to help structure user-submitted issues, or can be modified to suit the needs of data standard developers. We used these templates when establishing ESS-DIVE's community space on GitHub (https://github.com/ess-dive-community) that includes documentation for community-led data reporting formats. We also include file-level metadata 'flmd.csv' that describes the contents of each file within this data package. Lastly, the temporal range that we indicate in our metadata is the time range during which we searched for data standards documented on GitHub.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Data from: "A guide to using GitHub for developing and versioning data standards and reporting formats"

These data are the results of a systematic review that investigated how data standards and reporting formats are documented on the version control platform GitHub. Our systematic review identified 32 data standards in earth science, environmental science, and ecology that use GitHub for version control of data standard documents. In our analysis, we characterized the documents and content within each of the 32 GitHub repositories to identify common practices for groups that version control their documents on GitHub.In this data package, there are 8 CSV files that contain data that we characterized from each repository, according to the location within the repository. For example, in 'readme_pages.csv' we characterize the content that appears across the 32 GitHub repositories included in our systematic review. Each of the 8 CSV files has an associated data dictionary file (names appended with '_dd.csv' and here we describe each content category within CSV files.There is one file-level metadata file (flmd.csv) that provides a description of each file within the data package.

54 ENVIRONMENTAL SCIENCES↗