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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025)

Abstract The 56th meeting of the Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) was held in Bari, Italy, in July/August, 2024, and 115 submitted taxonomy proposals were reviewed. A total of 112 were subsequently ratified by the ICTV membership. An additional 9 error correction proposals were also approved in August 2025. This article lists the taxonomy proposals that have now been incorporated into release 40 version v2 of the Master Species List ( https://ictv.global/msl ), the Virus Metadata Resource ( https://ictv.global/vmr ), and associated ICTV databases. In addition to the assignments of 1,563 new virus species, 243genera, 55 families, 11 orders, and 8 classes, there were substantial additions to higher taxonomic ranks. These include the creation of a new realm ( Singelaviria ), which is based on the recognition of a separate evolutionary origin for the hallmark capsid genes of members of the kingdom Helvetiavirae. These express capsid proteins forming a single jelly-roll fold that is structurally and evolutionarily distinct from those of members of the family Bamfordvirae , assigned to the realm Varidnaviria . Furthermore, the realm Varidnaviria underwent a major reorganization, including the addition of a new kingdom, Abadenavirae . Another notable change was the classification of the vertebrate-infecting single-stranded DNA anellovirids into a new phylum Commensaviricota (kingdom Shotokuvirae , realm Monodnaviria ). Archaeal viruses infecting the hyperthermophilic Archaeoglobi were assigned to a new phylum Calorviricota , in the kingdom Trapavirae (realm Monodnaviria ), whereas RNA viruses infecting hyperthermophilic bacteria were classified into a new phylum Artimaviricota (realm Riboviria ). In recognition of his extensive and valuable contributions to virus taxonomic developments in Study Groups and over the period of his EC membership, Stuart Siddell was honoured as a new life member of the ICTV. The ICTV has created a new strategy for disseminating information on taxonomy advances through annual open-access publication of citeable taxonomy proposal summaries from each ICTV Subcommittee. A collective total of 354 co-authors of the seven summaries were drawn from members of each Subcommittee, the EC, and a very large number of contributors from the wider virology community.

Simmonds, Peter (ORCID:0000000279644700)↗
DOE OSTI2025

Prompt-Based Development of Domain-Specific Taxonomies

Framework for interacting with prompt-based LLMs (Large Language Models such as, but not limited to, ChatGPT) in order to develop domain specific taxonomies. The software itself is a series of prompts designed to extract hierarchical taxonomy categories from an LLM, as well as guidelines for how to fine-tune LLMs in order to provide better domain-specific taxonomic categories.

Grundy, Jon [Pacific Northwest National Laboratory↗
DOE OSTI2025

An HPC benchmark survey and taxonomy for characterization

The field of High-Performance Computing (HPC) is defined by providing computing devices with highest performance for a variety of demanding scientific users. The tight co-design relationship between HPC providers and users propels the field forward, paired with technological improvements, achieving continuously higher performance and resource utilization. A key device for system architects, architecture researchers, and scientific users are benchmarks, allowing for well-defined assessment of hardware, software, and algorithms. Many benchmarks exist in the community, from individual niche benchmarks testing specific features, to large-scale benchmark suites for whole procurements. We survey the available HPC benchmarks, summarizing them in table form with key details and concise categorization, also through an interactive website. For categorization, we present a benchmark taxonomy for well-defined characterization of benchmarks.

Benchmarking↗
DOE OSTI2024

Nonexhaustive Taxonomy of Hydropower and Pumped Storage Hydro Facilities [Slides]

The National Renewable Energy Laboratory (NREL) has published benchmark technical reports and presentations that disaggregate major product components for a variety of technologies, including land-based and offshore wind, photovoltaic, and battery energy storage systems. NREL has partnered with staff from the Pacific Northwest National Laboratory (PNNL) and members of the U.S. Department of Energy's Water Power Technology Office (WPTO) to create a non-exhaustive taxonomy of the major products and components of hydropower and pumped storage systems.

13 HYDRO ENERGY↗
DOE OSTI2025

A Taxonomy and Feature set for Server-Side Identification of Proxies

Malicious actors frequently use proxies and VPNs to evade detection and hide their origin. Current challenges to information security include the use of residential proxies to blend in with normal traffic and Man-in-the-Middle phishing proxies that are used to compromise accounts protected with mult-factor authentication. We advance a taxonomy and feature set for the identification of proxied traffic based on the network layer where proxying occurs. We describe how these features apply to common proxy types and how to use these features in the classification of the proxied traffic. Collection of these additional features is feasible using existing network sensors and web servers, while only adding about 30% volume to commonly deployed network sensor logs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A taxonomy of automatic differentiation pitfalls

Automatic differentiation is a popular technique for computing derivatives of computer programs. While automatic differentiation has been successfully used in countless engineering, science, and machine learning applications, it can sometimes nevertheless produce surprising results. In this paper, we categorize problematic usages of automatic differentiation, and illustrate each category with examples such as chaos, time-averages, discretizations, fixed-point loops, lookup tables, linear solvers, and probabilistic programs, in the hope that readers may more easily avoid or detect such pitfalls. We also review debugging techniques and their effectiveness in these situations.

Autodiff↗
DOE OSTI2025

Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota)

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.

Dirks, Alden C↗
DOE OSTI2026

A Proxy Method to Bridge LCA Data Gaps Using Automated Material Classification and Probabilistic Under-Specification

Life cycle assessments (LCAs) are essential for understanding the environmental impacts of material production. However, gaps in life cycle inventory (LCI) data for material and chemical inputs present a key challenge for LCA practitioners, especially in the early design stages. Strategies for filling in these gaps require additional time and expertise, which can hinder the LCA’s completion. This study combined automatic material classification and probabilistic under-specification to create a time-efficient method to fill material LCI data gaps. To illustrate the proposed method, proxy environmental impact distributions were generated using publicly available material LCI data classified into the ChemOnt chemical taxonomy using the open-source chemical classification software ClassyFire. Input materials with data gaps were then classified into the same taxonomy, where proxy environmental impact values could be selected from the available distributions to quickly fill in any data gaps. Although these methods were applied to classify material production processes available in the Federal LCA Commons and Ecoinvent databases, they can be applied to any LCA database. This study shows that classifying materials by their chemical structure produces taxonomies with increased granularity relative to industrial classification, improving the ability of under-specified proxy data to be used for differentiating the environmental impacts of competing designs.

biological databases↗
DOE OSTI2025

Bacterial response to the 2021 Orange County, California, oil spill was episodic but subtle relative to natural fluctuations

ABSTRACT An oil spill began in October 2021 off the coast of Orange County, California, releasing 24,696 gallons of crude oil into coastal environments. Although oil spills, such as this one, are recurrent accidents along the California coast, no prior studies have been performed to examine the severity of the local bacterial response. A coastal 10-year time series of short-read metagenomes located within the impacted area allowed us to quantify the magnitude and duration of the disturbance relative to natural fluctuations. We found that the largest change in bacterial beta-diversity occurred at the end of October. The change in taxonomic beta-diversity corresponded with an increase in the sulfur-oxidizing clade Candidatus Thioglobus, an increase in the total relative abundance of potential hydrocarbon-degrading bacteria, and an anomalous decline in the picocyanobacteria Synechococcus . Similarly, changes in function were related to anomalous declines in photosynthetic pathways and anomalous increases in sulfur metabolism pathways as well as aromatic degradation pathways. There was a lagged response in taxonomy and function to peaks in total PAHs. One week after peaks in total PAH concentrations, the largest shifts in taxonomy were observed, and 1 week after the taxonomy shifts were observed, unique functional changes were seen. This response pattern was observed twice during our sampling period, corresponding with the combined effect of resuspended PAHs and increased nutrient concentrations due to physical transport events. Thus, the impact of the spill on bacterial communities was temporally extended and demonstrates the need for continued monitoring for longer than 3 months after initial oil exposure. IMPORTANCE Oil spills are common occurrences in waterways, releasing contaminants into the aquatic environment that persist for long periods of time. Bacterial communities are rapid responders to environmental disturbances, such as oil spills. Within bacterial communities, some members will be susceptible to the disturbance caused by crude oil components and will decline in abundance, whereas others will be opportunistic and will be able to use crude oil components for their metabolism. In many cases, when an oil spill occurs, it is difficult to assess the oil spill’s impact because no samples were collected prior to the accident. Here, we examined the bacterial response to the 2021 Orange County oil spill using a 10-year time series that lies within the impacted area. The results presented here are significant because (i) susceptible and opportunistic taxa to oil spills within the coastal California environment are identified and (ii) the magnitude and duration of the in situ bacterial response is quantified for the first time.

Brock, Melissa L. (ORCID:0000000340329241)↗
DOE OSTI2025

Montane Conifer, Aspen, Meadow, and Sagebrush Metagenome Resolved Genomes and Traits in East River Watershed, Colorado, USA

Climate change is driving vegetation shifts in mountain watersheds, with unknown impacts on biogeochemical cycles. We hypothesize that these shifts will reshape soil microbiomes and associated biogeochemical processes. As a part of Lawrence Berkeley National Laboratory (LBNL) Watershed Science Focus Area (SFA), we assessed microbiome and microbial functional trait differences between soils under conifer, aspen, forby meadows, and sagebrush across the East River Watershed, CO, controlling for elevation and aspect.Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from soils 0-20cm in depth across three locations in the watershed—Headwaters, Upper Reaches, and Lower Reaches from August 3-11th 2016. Each location was further subdivided into two blocks, with one block on a west facing aspect, and two on the east aspect of the valley. Within blocks, two samples per vegetation type were taken (one at each depth). This resulted in 66 samples, which were sequenced at JGI and can be found under the Joint Genome Institute (JGI) Genomes Online Database (GOLD) sequencing project Gs0118068. Metagenomes were assembled through an inhouse pipeline (see methods), binned using four autobinners (concoct, maxbin2, metabat2, and vamb) and consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>75%) and contamination (<25%), and dereplicated at 95% ANI using drep. The dataset includes a zip file of 687 genomes (Vegtype_MAGS.zip), the accession numbers for the underlying metagenomes, a csv file with MAG quality metrics and taxonomy from Genome Taxonomy Database (GTDB) and National Center for Biotechnology Information (NCBI) taxonomic representative genome proteins (EastRiver_Vegtype_drep_genome_info.csv), and a file containing MAG quality metrics and taxonomy (gtdb_drep_bin_taxonomy.csv). The dataset additionally includes a sample metadata file (EastRiver_Vegtype_sample_metadata.csv), a metadata file used to register associated samples with IGSNs (International Generic Sample Numbers) (samples.csv), a Google KML file for the sampled locations (sample_collection_sites.kml), a location metadata file (locations.csv), a file-level metadata file (flmd.csv), and a data dictionary (dd.csv) file.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Common occupational classification system amendments for Accelerator Science and Engineering workforce

A common system to classify occupations and skills is essential to support accelerator workforce planning between the Department of Energy (DOE) National Laboratories. In 2025, ten DOE laboratories conducted a census of their accelerator science and engineering workforce and projected their accelerator workforce needs for the next ten years. To support this, revision 3 of the “Common Occupational Classification System” (COCS) was used as a common taxonomy. Modifications were made to include accelerator-specific skills and specialisms. COCS was originally developed for DOE Office of Environmental Restoration and Waste Management in 1996. The framework provides a high-level functional structure that can be expanded with further occupations and specialisms and remains well aligned to DOE laboratory roles nearly 30 years later. Accelerator occupations and specialisms were added to the framework for the 2025 effort to quantify the accelerator workforce. This document is a companion document to COCS and provides a definition for these new occupations and specialisms that do not appear in COCS. Proceeding with a stable taxonomy is seen as essential such that its use becomes easier each year; the taxonomy as used for the 2025 effort is recommended to be continued.

43 PARTICLE ACCELERATORS↗
DOE OSTI2026

Facilitating Data Collection of Maintenance Events to Populate the Hydrogen Component Reliability Database (HyCReD)

The Hydrogen Component Reliability Database (HyCReD) is a collaborative project between the National Renewable Energy Laboratory, the University of Maryland, and hydrogen stakeholders to improve safety and reliability for hydrogen facilities by implementing component reliability data taxonomies that support hydrogen infrastructure failure rate analysis. The project aims to quantify failure rates of hydrogen components through high-quality data collection and analysis on root causes and maintenance needed. HyCReD provides a common database for cataloging hydrogen component failures which exists for reliability research in many other mature industries [2]. The database fills a gap for the hydrogen community by providing a scientifically rigorous approach to quantitative risk assessment (QRA), prognostic health management (PHM), and reliability-centered maintenance (RCM) analysis. High level results will be aggregated and anonymized to protect company sensitive information; detailed results will be used to help address issues of hydrogen components. These advanced analytics will support accelerated deployment of hydrogen infrastructure by enabling better: design and safety of projects (safety codes and standards development), infrastructure reliability and cost (component failure rates, maintenance protocols), and component R&D needs (robust supply chain). A key to a successful HyCReD implementation is facilitating the ease of reporting and data quality in the database that can be used for analysis. Maintenance data was a previously identified gap in initial efforts to populate and validate the database taxonomies [3]. Collection of maintenance data will be instrumental in identifying failure modes and rates, identifying incipient component failures or reduced performance, cataloging best practices for maintenance routines and methods for prognostic health management, and quantifying the risk and effect of different failure modes. Several key priorities are identified for streamlined data collection to achieve quality and detailed failure data: Applicability, Ease of Use, Accessibility, and Information Security. The HyCReD team has now begun deployment of the database to several companies and groups that have signed non-disclosure agreements to facilitate the data collection of failures in industry hydrogen refueling station infrastructure. This paper will provide an update into the process of HyCReD deployment including the development of a coding guide for facility personnel to reference and ensure data quality and consistency from one station to another as well as implementation of contextually dependent data fields of system taxonomy and formatted entries to provide ease of use. The goal is to communicate the lessons learned from the roll-out to technicians and engineers in the field, and the addition of need for high level of security to protect all stakeholders.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗