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At least 325 records · Page 18

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DOE OSTI2024

KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Decontamination through Metagenomic Fractionation and analysis of Metabolic Potential-

Deep-sea microbiomes sampled with traditional or pressure-retaining instrumentation A fundamental property of life in the sea is that with increasing depth must come increased adaptation to elevated hydrostatic pressures. This project aims to assess technology for the accurate characterization of microbial biodiversity and biochemistry at greater depths, and validate its use in some of the deepest and least-explored waters in the Ocean: Hadal Trench. Compared to the 0.1 megapascal (MPa) of surface waters, organisms inhabiting at the average depth of the Ocean (3800 m) have to deal with pressures of 38 MPa (5,500 psi). The effects of these high pressure have been most thoroughly investigated in microorganisms, where it has been found to affect membrane integrity and transport, cytoskeletal assembly and both DNA and protein synthesis. We will explore the diversity and activity of microorganisms from 2000 m to >8,000 m depths within the highly productive water column of hadal trenches, comparing seawater samples obtained with and without substantial pressure changes during recovery. A pressure retaining device was used to sample the microbial communities of the watercolumn with reduced decompression during retreival (Peoples et. al., 2019). References: Peoples LM, Norenberg M, Price D, McGoldrick M, Novotny M, Bochdansky A, Bartlett DH. A full-ocean-depth rated modular lander and pressure-retaining sampler capable of collecting hadal-endemic microbes under in situ conditions. Deep Sea Research Part I: Oceanographic Research Papers. 2019 Jan 1;143:50-7.

Plominsky, Alvaro M.↗

DOE OSTI2024

KBase Narrative - Metabolic_reconstruction_ETDI_mangrove

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

Laux, Marcele↗

DOE OSTI2024

KBase Narrative - Atacama Trench & Sn Clemente 2018 cruise Metagenomes -Sequence quality filtration & Assembly-

Plominsky, Alvaro M.↗

DOE OSTI2026

Mapping the soil microbiome functions shaping wetland methane emissions

Accounting for only 8% of Earth’s land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.

MAG↗

DOE OSTI2020

Validation of ORIGEN for VVER-440 Spent Fuel with Application to Fork Detector Safeguards Measurements

The US Department of Energy National Nuclear Security Administration and the European Atomic Energy Community (Euratom) are collaborating with the Radiation and Nuclear Safety Authority in Finland to assess spent fuel verification methods for potential application to measurements at the planned spent fuel encapsulation plant and geological repository prior to final disposal in Finland. The fork detector (FDET) used to measure the neutron and gamma radiation from a given spent fuel assembly is an existing technology widely used by the International Atomic Energy Agency (IAEA) and Euratom for the safeguards verification of spent fuel operator declaration. Recently, an FDET data analysis software, referred to as the ORIGEN module, was developed and incorporated into the IAEA/Euratom Integrated Review and Analysis Program. This module uses the ORIGEN burnup code to calculate the nuclide concentrations and the neutron and gamma source terms in the spent fuel based on operator declarations. Then, to predict the expected FDET signals for a given fuel assembly, the module combines the source terms calculated by ORIGEN with FDET response functions that were pre-generated using MCNP models. The inspector can compare the calculated signals to the measured values in real time to identify possible anomalies in fuel assembly’s operator declaration, integrity, or measurement. In this work, the capability of the ORIGEN module was extended from application to typical light water reactor fuels to use for VVER-440 assembly types. The accuracy of ORIGEN for this type of fuel assembly calculations was assessed by comparing calculated nuclide concentrations against destructive assay measurements for VVER-440 spent fuel. The performance of the ORIGEN module for FDET safeguards verification in routine inspections was assessed using FDET measurement data for 13 spent VVER-440 assemblies that were measured at the Loviisa Nuclear Power Plant in Finland, by comparing the calculated signals to the measured quantities. The results show that the calculated FDET neutron and gamma detector signals are generally within 12% of the measurements except for one assembly. Thus, these results are applicable to future safeguards verification in the planned Finland encapsulation plant, such as for passive neutron albedo reactivity safeguards measurements.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2024

The microbiome of a Pacific moon jellyfish Aurelia coerulea

The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea, first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca. Mariplasma lunae (Mollicutes) and Ca. Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca. Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Survey of Use Cases and Scenarios on the Open Energy Data Initiative Solar Systems Integration (OEDI SI) Platform

The Open Energy Data Initiative Solar Systems Integration (OEDI SI) Data and Modeling Platform offers a comprehensive set of use cases tailored for power systems analysis. Each use case is centered around a specific power system analysis problem, supported by composite input data and reference algorithms. These composite input datasets are meticulously assembled using OEDI SI's data preprocessing tools, which integrate raw data from various sources. The primary objectives of the OEDI SI Platform include facilitating access to composite input data through widely accepted input/output formats and verified results. This accessibility enables power system network researchers and developers to validate their algorithms and showcase their applications' capabilities to the broader community. Moreover, the platform strives to promote reproducible, robust, replicable, and generalizable solar systems integration research.

14 SOLAR ENERGY↗

DOE OSTI2023

Neutron Calibration Studies for the SuperCDMS SNOLAB Experiment

My time at Fermilab has been dedicated to advancing the field of dark matter detection through my contributions to the SuperCDMS collaboration. The first project involved the development and testing of a delivery system for a Cf-252 neutron source to calibrate the SuperCDMS silicon and germanium detectors. Subsequently, I focused on parametrizing the detectors' instrumental response by optimizing a plastic scintillator backing array to measure the scattering angle of a collimated neutron beam. The Monte Carlo simulation I designed provided insights into the detection efficiency of the array, and the best-fit design I arrived at for the scattering counters will be implemented into the final array. Additionally, I assembled a muon detector with legacy hardware to enhance the ability of the calibration experiment to reduce dark current and false signals. As my work nears completion, I am confident that these contributions will significantly enhance the precision and reliability of the SuperCDMS experiment, pushing the boundaries of our understanding of dark matter and contributing to the broader scientific community's quest to unravel the mysteries of the universe.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Testing nuclear data libraries with burnup for reactor applications

Recently US and European nuclear data libraries have been released, namely ENDF/B-VIII.0 and JEFF-3.3 libraries, which are the result of years of evaluation and validation work in both communities. Consequently, efforts have been made to validate the evaluations in calculations of integral experiments (critical benchmarks, ..etc). Nevertheless, less stringent testing and validation efforts were performed on burnup applications before releasing the libraries. The presented work focusses on the testing of these recent nuclear data libraries for burnup calculations on two benchmarks at the pin and at the assembly level. Monte-Carlo depletion calculations were performed using the VESTA 2.2 code. The K{sub ∞} results between nuclear data libraries are compared. A strong k{sub ∞} bias is observed with burnup using both JEFF-3.3 and JEFF-4T0 compared to all other libraries, and especially ENDF/B-VIII.0, consisting in a strong k{sub ∞} over-estimation at low burnup and a high under-estimation at high burnup. JEFF-3.3 {sup 235}U and {sup 239}Pu evaluations mainly explain this result, as well as fission yields. New {sup 235}U and {sup 239}Pu evaluations were proposed for JEFF-4T0, but they do not address totally the bias issue, even if JEFF-4T0 {sup 239}Pu allows slightly reducing the k{sub ∞} underestimation at high burnup.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Joining technique for in-oven/autoclave molds manufactured by large scale polymer additive manufacturing

Large scale additive manufacturing (AM) of fiber-reinforced polymer composites has gained traction in the mold and die community over the last decade, largely due to reduced material cost and lead time. However, limitations in mold size remain present due to printer volume constraints and costs associated with large format machines. Here, this paper describes a method for producing additively manufactured polymer molds in segments with an O-ring joint design, which can be machined and subsequently assembled for autoclave applications. The developed joining mechanism allows for maintaining the vacuum integrity during the cure cycle while accounting for the anisotropic nature of the additively manufactured polymer molds. Over a range of tested temperatures, 20–200 °C, the multi-part mold joining design was able to achieve full vacuum of ∼73.7 cmHg (29 inchHg) and maintain a vacuum integrity with vacuum losses less than 1.5 cmHg/5min (0.6 inchHg).

Joining↗

DOE OSTI2022

Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles. Our dataset represents 3635 metagenome-assembled genomes encompassing 511 novel and recently identified genera from deep-sea hydrothermal settings. Some of the novel bacterial (107) and archaeal genera (30) that were recently reported from the deep-sea Brothers volcano were also detected at the deep-sea hydrothermal vent fields, while 99 bacterial and 54 archaeal genera were endemic to the deep-sea Brothers volcano deposits. We report some of the first examples of medium- (≥ 50% complete, ≤ 10% contaminated) to high-quality (> 90% complete, < 5% contaminated) MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur, and hydrogen metabolic processes across all sites and illustrates sulfur and nitrogen metabolic “handoffs” in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment. Our study of globally distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms

Massive releases of organic substrates during marine algal blooms trigger growth of many clades of heterotrophic bacteria. Algal polysaccharides represent the most diverse and structurally complex class of these substrates, yet their role in shaping the microbial community composition is poorly understood. We investigated, whether polysaccharide utilization capabilities contribute to niche differentiation of Polaribacter spp. (class Flavobacteriia; known to include relevant polysaccharidedegraders) that were abundant during 2009–2012 spring algal blooms in the southern North Sea. We identified six distinct Polaribacter clades using phylogenetic and phylogenomic analyses, quantified their abundances via fluorescence in situ hybridization, compared metagenome-assembled genomes, and assessed in situ gene expression using metaproteomics. Four clades with distinct polysaccharide niches were dominating. Polaribacter 2-a comprised typical first responders featuring small genomes with limited polysaccharide utilization capacities. Polaribacter 3-a were abundant only in 2010 and possessed a distinct sulfated α-glucoronomannan degradation potential. Polaribacter 3-b responded late in blooms and had the capacity to utilize sulfated xylan. Polaribacter 1-a featured high numbers of glycan degradation genes and were particularly abundant following Chattonella algae blooms. These results support the hypothesis that sympatric Polaribacter clades occupy distinct glycan niches during North Sea spring algal blooms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Five draft genome assemblies from Bacillaceae isolated from a degraded wetland environment

Abstract We isolated 5 Bacillaceae from a degraded wetland environment and sequenced their genomes using Illumina NextSeq. Here, we report draft genome sequences of Bacillus velezensus-SC119, Priestia megaterium-SC120, Bacillus zhangzhouensis-SC123, Bacillus pumilis-SC124, and Bacillus idriensis-SC127. The genomes range between 3,657,353 and 5,772,725 base pairs with %GC between 37.62% and 46.38%. Introduction Wetland environments play critical roles in the terrestrial carbon and water cycles and microbial communities are key players in healthy ecosystem function. Endospore forming bacteria in the Bacillaceae family are metabolically and genomically diverse soil heterotrophs that influence plant health, carbon and nitrogen cycling, and often produce diverse natural products that influence other bacterial and non-bacterial species in their environment (1). We collected two soil samples on January 19, 2023 from 42°43'12.7"N 73°45'01.4"W. One was highly hydrated and within a patch of invasive common reeds (Phragmites sp.) and the other was near the base of an Eastern cottonwood tree (Populus deltoides). Bacillus pumilis strain SC124 was isolated from the soil from near the cottonwood tree, while Bacillus velezensis strain SC119, Priestia megaterium strain SC120, Bacillus zhangzhouensis strain SC123, Bacillus idriensis strain SC127 and were isolated from the marshy soil.

isolate, wetlands, genome announcement↗

DOE OSTI2021

Fork Experiments in the Hot Cell Using Spent Fuel Rods for International Nuclear Safeguards

This work leveraged the rare availability of 25 full-length pressurized water reactor spent fuel rods and 1 irradiated mixed-oxide rod at an Oak Ridge National Laboratory hot cell. This was done to collect measurement data with two Fork detectors to assess the detectors’ capability of verifying operator declaration data and detecting partial defects in spent fuel, which are the two primary goals of international safeguards on spent nuclear fuel. The data can also be used to benchmark the ORIGEN module, which has been adopted in the International Atomic Energy Agency’s (IAEA’s)/European Atomic Energy Community’s (Euratom’s) Integrated Review and Analysis Program to predict the Fork detector count rates in real time. In this project, the authors first calibrated two Fork detectors—a standard one and a modified one—by using known strong neutron and gamma sources. Then, the authors measured all 26 fuel rods at multiple locations along the length. The fuel rods were then assembled into three arrays—2 × 2, 3 × 3, and 5 × 5—by using specially designed support grids to mimic fuel assemblies and measure the arrays with both detectors. For the 5 × 5 array, 4 and 8 fuel rods of the array were replaced in two separate cases with short stainless-steel rods to mimic two partial defect scenarios, and the arrays were measured before and after the replacements. Polyethylene blocks were used in this experiment to mimic water. The results show that the Fork detectors were able to verify operator declarations and detect partial defects in spent fuel, and the authors were the first to demonstrate this through experiments. A discovery was also made that determined the root cause of the nonlinear response to gamma dose in the ion chambers used in IAEA and Euratom’s Fork detectors. After the experiments, both detectors were retrieved from the hot cell for future use. The data collected in this project will be used in a parallel International Nuclear Safeguards Engagement Program (INSEP) project to enhance the safeguards in the Finnish spent fuel encapsulation plant, and the data will be useful to other projects in the future given the increased safeguards needs due to spent fuel transfer and disposal activities worldwide.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages

Cryptoendolithic communities are microbial ecosystems dwelling inside porous rocks that are able to persist at the edge of the biological potential for life in the ice-free areas of the Antarctic desert. These regions include the McMurdo Dry Valleys, often accounted as the closest terrestrial counterpart of the Martian environment and thought to be devoid of life until the discovery of these cryptic life-forms. Despite their interest as a model for the early colonization by living organisms of terrestrial ecosystems and for adaptation to extreme conditions of stress, little is known about the evolution, diversity, and genetic makeup of bacterial species that reside in these environments. Using the Illumina Novaseq platform, we generated the first metagenomes from rocks collected in Continental Antarctica over a distance of about 350 km along an altitudinal transect from 834 up to 3100 m above sea level (a.s.l.). A total of 497 draft bacterial genome sequences were assembled and clustered into 269 candidate species that lack a representative genome in public databases. Actinobacteria represent the most abundant phylum, followed by Chloroflexi and Proteobacteria. The “Candidatus Jiangella antarctica” has been recorded across all samples, suggesting a high adaptation and specialization of this species to the harshest Antarctic desert environment. The majority of these new species belong to monophyletic bacterial clades that diverged from related taxa in a range from 1.2 billion to 410 Ma and are functionally distinct from known related taxa. Our findings significantly increase the repertoire of genomic data for several taxa and, to date, represent the first example of bacterial genomes recovered from endolithic communities. Their ancient origin seems to not be related to the geological history of the continent, rather they may represent evolutionary remnants of pristine clades that evolved across the Tonian glaciation. These unique genomic resources will underpin future studies on the structure, evolution, and function of these ecosystems at the edge of life.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Assessing fuel cycle design options for advanced microreactors

Microreactor (MR) technology have recently gained traction due to their reduced construction cost compared to traditional large reactors. Their small physical geometry results in increased neutron leakage and deteriorated neutron economy which limits the achievable burnup of MR fuel. Refueling strategy currently discussed in MR design community is the battery-like refueling which is involve replacing the entire reactor core at the end of their operational cycle. Here, this paper investigates partial core refueling as means to increase MR fuel burnup and improve fuel cycle economy as a result. Two fuel cycle design strategies have been successful. These are the partial core refueling and partial core refueling combined with assembly rotation. Both strategies have been tested to operate a heatpipe-cooled MR referred to as the eVinci-like core for 72 Effective Full Power Months (EFPMs). The partial core refueling showed to reduce the refueling requirements by 18% compared to the battery-like refueling strategy. This corresponds to 10.5% reduction in the Net Present Value (NPV) of fuel cost over the 72 EFPMs of operation. The partial core refueling combined with rotation case reduces the refueling requirements by 29% (corresponding to 14.5% reduction in NPV of fuel cost) compared to the battery-like refueling strategy.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2026

Finding the missing pieces: filling gaps that impede the translation of omics data into models

High-throughput omics technologies such as DNA sequencing have made the sequencing and computational assembly of microbial genomes recovered from the environment relatively routine. Computational inference of the protein products encoded by these genomes, and the associated biochemical functions, should enable the accurate prediction and modeling of microbial metabolism, organismal interactions, and ecosystem processes. However, a lack of scalable, probabilistic protein annotation tools limits the full potential of modeling for understanding the metabolism and biogeochemical cycles of microbial communities. Our approach to improve inference of protein annotations and metabolic models relied on learning from and emulating expert manual curation, leveraging software engineering and data science best practices to scale up the throughput and accuracy of annotations and metabolic model construction, building software to objectively evaluate different annotation strategies, and more closely linking the protein annotation and metabolic model inference process. Outcomes of this research include several improved or new computational tools, including DRAM (Distilled and Refined Annotation of Metabolism) for annotating microbial genomes with protein function and metabolic traits, CAMPER (Curated Annotations for Microbial Polyphenol Enzymes and Reactions) for annotating key polyphenol metabolisms, EC-Bench for comprehensive and unbiased benchmarking of annotation tools, and several apps available via the DOE Systems Biology Knowledgebase (KBase) for building genome-scale metabolic models. We demonstrate that these tools allow us to scalably annotate and understand thousands of genomes for microbial communities from a variety of systems and test cases, including rivers, thawing permafrost, and gut microbiomes. All of these computational tools are available as open-source software, with most broadly and easily accessible to the scientific community via KBase apps.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Soil microbiome engineering for sustainability in a changing environment

Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth’s soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗