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DOE OSTI2026

Extracellular DNA Alters Detection of Subtle Bacterial Responses to Soil Rewetting

Microbial communities are often characterized using DNA-based sequencing, but these approaches also capture extracellular DNA (exDNA) released from dead cells, potentially altering inference about microbial responses to environmental change. This may be especially important during pulse disturbances, such as soil drying–rewetting, which can increase microbial mortality and transient necromass pools. We assessed whether exDNA altered inference about bacterial responses to drying–rewetting (an 80 mm simulated rainfall event following a 28-day drought) in conventionally tilled corn and perennial switchgrass soils. We quantified bacterial abundance (16 S rRNA gene copies), alpha diversity, and community composition in paired soil samples with exDNA included (+ exDNA) and in samples treated with propidium monoazide (PMAxx) to reduce amplification of exDNA (− exDNA). At our level of replication (n = 4), PMAxx treatment did not significantly alter overall temporal response patterns (i.e., no significant main effect of DNA treatment or DNA × time interaction). However, PMAxx treatment increased sensitivity to detect some pairwise temporal changes in bacterial abundance and community composition in corn soils following rewetting. exDNA pools were proportionally highest immediately after rewetting in corn soils, suggesting transient extracellular DNA may contribute to masking during disturbance recovery. In contrast, PMAxx treatment had comparatively small effects in switchgrass soils, which exhibited weaker temporal responses overall. Inclusion of exDNA also changed which taxa appeared most responsive to rewetting. Together, our results suggest that exDNA does not uniformly bias soil microbial inference, but may reduce detectability of subtle disturbance-driven shifts in certain soils. Future studies should advance knowledge of microbial turnover and necromass dynamics, particularly using multiple complementary methods, to help predict when exDNA is most likely to influence ecological inference.

drying-rewetting↗

DOE OSTI2017

Soap production: A green prospective

Highlights: • Reducing the amount of different types of municipal waste. •Recycling waste to obtain a useful green soap, which is good quality and cheap. • Inspiring community projects meant to convey recycling and ecological approach. • Contributing to families’ economy and stimulating the use of healthier products. - Abstract: A green prospective based on the reuse of waste materials such as almond shells, orange peel and used cooking oil to manufacture soap is presented. In Portugal, thousands of tons of waste are generated from used cooking oil and production of nut shells’ residues is growing every year. In addition, the high consumption of citrus fruits, oranges in particular, generates large amounts of citrus peel. Therefore, it is necessary to diversify reuse mechanisms of these wastes, in order to make them back into raw materials. Complying with this trend, this work was carried out by processing and grinding almond shells, treating used oil, processing orange peels and extracting limonene, formulating and producing soap, and performing an acceptance study of the final product. Results validated a high potential of the idea in the field of environmental education, so it can be replicated in practical classes. It can also be useful for waste management, and it can support the development of community projects on an ecological approach.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Integration and Quantitative Comparison of Up-Scaled Molecular Observation Network Data with Existing Soil Databases

MONet provides novel soil molecular data to the research community for understanding biogeochemical processes and complementing other soil datasets. This study assesses MONet's ability to replicate known soil patterns via a comparative analysis of soil respiration (Rs), pH, and clay content against benchmark datasets. Results show moderate agreement for pH and clay content, highlighting MONet's strengths in capturing soil biogeochemical variation in underrepresented regions like urban areas. Rs data are marked by the appropriate trends relative to other datasets, but direct comparison is impractical due to methodological differences in underlying data. Strategic sampling is recommended to improve MONet's coverage and eventual utility in bridging molecular observations with global datasets.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

A metagenomic survey of forest soil microbial communities more than a decade after timber harvesting

The scarcity of long-term data on soil microbial communities in the decades following timber harvesting limits current understanding of the ecological problems associated with maintaining the productivity of managed forests. The high complexity of soil communities and the heterogeneity of forest and soil necessitates a comprehensive approach to understand the role of microbial processes in managed forest ecosystems. Here, we describe a curated collection of well replicated, multi-faceted data from eighteen reforested sites in six different North American ecozones within the Long-term Soil Productivity (LTSP) Study, without detailed analysis of results or discussion. The experiments were designed to contrast microbial community composition and function among forest soils from harvested treatment plots with varying intensities of organic matter removal. The collection includes 724 bacterial (16S) and 658 fungal (ITS2) amplicon libraries, 133 shotgun metagenomic libraries as well as stable isotope probing amplicon libraries capturing the effects of harvesting on hemicellulolytic and cellulolytic populations. This collection serves as a foundation for the LTSP Study and other studies of the ecology of forest soil and forest disturbance.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters

The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood–Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community’s capacity, with up to 9.9% of fermentation, 6.4% of the Wood–Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.

Candidatus↗

DOE OSTI2022

Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition

Protists, in particular bacterivores, are essential players in the rhizosphere; thus, how their interactions with bacteria and fungi affect plant productivity and soil nutrient cycles warrants more attention. Using next-generation sequencing of the 18 S rRNA gene, we investigated the distribution of two major protistan phyla, Cercozoa and Endomyxa, across four seasons, and four soil compartments - rhizosphere, root, soil and litter. The sampling was replicated in two forests in Norway and the Czech Republic, in order to test our results across biogeographic scales. Compartment had a major influence in shaping protistan communities, over and above spatial distance and seasonal variation. Protistan diversity was highest in the bulk soil while lowest in the roots, suggesting that the plants select for restricted assemblages of protists. Accordingly, only the root compartment harboured a subset of the bulk soil protistan diversity. In addition, protistan communities showed markedly different distributions according to their feeding modes, with opposite patterns for bacterivores versus omnivores and eukaryvores. The small bacterivorous flagellates (mostly Glissomonadida) were more abundant in roots, while the larger amoeboid eukaryvores (e.g. some of the Cryomonadida and vampyrellids) dominated in soil and in the rhizosphere, and the omnivores (e.g. Euglyphida and part of the Cercomonadida), also large and mostly amoeboid, were more abundant in litter. The current view of the soil microbiome is mostly focused on bacteria and fungi: this detailed study on the community distribution of protists according to their feeding modes reveals the essential role they play in each of the soil compartments, an essential precondition for a detailed understanding of the soil food web and nutrient cycling in forest.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Applying Social Science Methods to Assess and Improve Program Outcomes: A Case Study on the Gap Region Outreach Project

This paper outlines a replicable framework for assessing gaps, reach, and the impact of technical assistance (TA) programs, using the Energy to Communities (E2C) Gap Region Outreach Project as a case study. By applying qualitative social science methods, this framework provides tools for effectively engaging with underrepresented regions, identifying barriers to participation, and tailoring solutions to local needs. The study highlights the importance of leveraging stakeholder insights to address disparities in program engagement and participation, offering actionable recommendations to enhance program responsiveness and optimize resource allocation. This approach serves as a guide for practitioners seeking to expand the reach and effectiveness of federally funded TA programs while ensuring alignment with community priorities and capacity needs.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2018

Distributed Energy Planning for Climate Resilience

At various levels of government across the United States and globally climate resilient solutions are being adopted and implemented. Solutions vary based on predicted hazards, community context, priorities, complexity, and available resources. Lessons are being learned through the implementation process, which can be replicated regardless of level or type of government entity carrying out the resiliency planning. Through a number of analyses and technical support across the world, NREL has learned key lessons related to resilience planning associated with power generation and water distribution. Distributed energy generation is a large factor in building resilience with clean energy technologies and solutions. The technical and policy solutions associated with distributed energy implementation for resilience fall into a few major categories, including spatial diversification, microgrids, water-energy nexus, policy, and redundancy.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2019

Best Practices in Resilience Planning

At various levels of government across the United States and globally, resilience solutions are being adopted and implemented. Solutions vary based on predicted hazards, community context, priorities, complexity, and available resources. Lessons are being learned through the implementation process, which can be replicated, regardless of level or type of government entity carrying out the resilience planning. Through a number of analyses and technical support activities across the world, NREL has learned key lessons related to resilience planning associated with power generation and water distribution. Distributed energy generation is a large factor in building resilience with clean energy technologies and solutions.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2023

Nitrogen addition alters soil fungal communities, but root fungal communities are resistant to change

Plants are colonized by numerous microorganisms serving important symbiotic functions that are vital to plant growth and success. Understanding and harnessing these interactions will be useful in both managed and natural ecosystems faced with global change, but it is still unclear how variation in environmental conditions and soils influence the trajectory of these interactions. In this study, we examine how nitrogen addition alters plant-fungal interactions within two species of Populus - Populus deltoides and P. trichocarpa. In this experiment, we manipulated plant host, starting soil (native vs. away for each tree species), and nitrogen addition in a fully factorial replicated design. After ~10 weeks of growth, we destructively harvested the plants and characterized plant growth factors and the soil and root endosphere fungal communities using targeted amplicon sequencing of the ITS2 gene region. Overall, we found nitrogen addition altered plant growth factors, e.g., plant height, chlorophyll density, and plant N content. Interestingly, nitrogen addition resulted in a lower fungal alpha diversity in soils but not plant roots. Further, there was an interactive effect of tree species, soil origin, and nitrogen addition on soil fungal community composition. Starting soils collected from Oregon and West Virginia were dominated by the ectomycorrhizal fungi Inocybe (55.8% relative abundance), but interestingly when P. deltoides was grown in its native West Virginia soil, the roots selected for a high abundance of the arbuscular mycorrhizal fungi, Rhizophagus. These results highlight the importance of soil origin and plant species on establishing plant-fungal interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Communities of the Future: Accelerating Zero Energy District Master Planning: Preprint

Zero energy districts aggregate multiple buildings and optimize energy efficiency, district thermal energy, and renewable energy generation among those buildings so that on-site renewable energy can offset the energy use at a district scale. Zero energy districts have the potential to dramatically improve the economic competitiveness, resiliency, environmental quality, and energy independence of communities. The U.S. Department of Energy (DOE) Zero Energy Districts Accelerator (ZEDA) brings together district developers, planners, owners, national experts, and key stakeholders to develop the energy master planning documents needed for zero energy district development and replication. Through this effort, DOE is working with pioneering leaders to understand and address barriers to achieving zero energy districts. Each district partner will complete detailed energy master plans that provide the framework necessary to achieve ambitious energy goals. These complex projects represent billions of dollars of investment and are creating the communities of the future. ZEDA partners are using best-practice approaches to realize energy performance goals for the entire building and district life cycle. Their successful strategies will be documented and made available to promote replication in cities around the world that are setting aggressive energy goals. This paper introduces zero energy districts, reviews the structure of ZEDA, discusses the value of energy master planning, presents barriers to zero energy districts and how these are being addressed by zero energy district pioneers, and suggests pathways for wide-scale replication.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2018

Communities of the Future: Accelerating Zero Energy District Master Planning

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2017

SPRUCE Deep Peat Microbial Diversity, CO2 and CH4 Production in Response to Nutrient, Temperature, and pH Treatments during Incubation Studies

This dataset contains the results of a microcosm incubation study on deep peat collected from the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experimental site within the Marcell Experimental Forest in northern Minnesota, USA in September 2014. Microcosms were monitored for carbon dioxide (CO2) and methane (CH4) production, and microbial community dynamics were assessed using quantitative polymerase chain reaction (qPCR) and amplicon sequencing. The experiment was designed with a full factorial design with elevated temperature, nitrogen (N), (P), and pH treatments was used with samples from each transect serving replicates. In all, 96 microcosms were constructed to account for the 16 treatment combinations (Nitrogen x Phosphorous x pH x temperature), 2 time points, and 3 replicates. Temperature treatments were 6 degrees C, to mimic the SPRUCE ambient plot temperatures, and 15 degrees C to mimic the SPRUCE +9 degrees C treatment. These data show that one year of deep peat warming, microbial community structure and abundance of bacterial, archaeal, fungal, and methanogenic populations showed strong vertical stratification across the peat depth profile yet no clear response to the temperature treatments (Kluber et al, 2020). In an effort to identify factors that may be limiting decomposition and microbial community change in deep peat, we conducted an anerobic microcosm incubation of deep peat (150-200 cm depth). This dataset contains one data file in comma-separate values (*.csv) format. Additional metadata are provided: a data dictionary and a file-level metadata file in comma-separate values (.csv) format and a user guide in PDF (*.pdf) format.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Disturbance: a double-edged sword for restoration in a changing climate

Ecological restoration often relies on disturbance as a tool for establishing target plant communities, but disturbance can be a double-edged sword, at times initiating invasion and unintended outcomes. Here, in this study, we test how fire disturbance, designed to enhance restoration seeding success, combines with climate and initial vegetation conditions to shift perennial versus annual grass dominance and overall community diversity in Pacific Northwest grasslands. We seeded both native and introduced perennial grasses and native forbs in paired, replicated burned-unburned plots in three sites along a latitudinal climate gradient from southern Oregon to central-western Washington. Past restoration and climate manipulations at each site had increased the variation of starting conditions between plots. Burning promoted the expansion of extant forbs and perennial grasses across all sites. Burning also enhanced the seeding success of native perennial grass and native forbs at the northern and central site, and the success of introduced perennial grasses across all three sites. Annual grass dominance was driven more by latitude than burning, with annuals maintaining their dominance in the south and perennials in the north. At the same time, unrestored grasslands surrounding all sites remained dominated by perennial grasses, suggesting that initial plot clearing may have allowed for annual grass invasion in the southern site. When paired with disturbance, further warming may increase the risk of annual grass dominance, a potentially persistent state.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

dCache on Steroids - Delegated Storage Solutions

For over a decade, dCache.org has delivered a robust software used at more than 80 Universities and research institutes around the world, allowing these sites to provide reliable storage services for the WLCG experiments as well as many other scientific communities. The flexible architecture of dCache allows running it in a wide variety of configurations and platforms - from a SoC based all-in-one Raspberry-Pi up to hundreds of nodes in a multipetabyte installation. Due to lack of managed storage at the time, dCache implemented data placement, replication and data integrity directly. Today, many alternatives are available: S3, GlusterFS, CEPH and others. While such solutions position themselves as scalable storage systems, they cannot be used by many scientific communities out of the box. The absence of community-accepted authentication and authorization mechanisms, the use of product specific protocols and the lack of namespace are some of the reasons that prevent wide-scale adoption of these alternatives. Most of these limitations are already solved by dCache. By delegating low-level storage management functionality to the above-mentioned new systems and providing the missing layer through dCache, we provide a solution which combines the benefits of both worlds - industry standard storage building blocks with the access protocols and authentication required by scientific communities. In this paper, we focus on CEPH, a popular software for clustered storage that supports file, block and object interfaces. CEPH is often used in modern computing centers, for example as a backend to OpenStack services. We will show prototypes of dCache running with a CEPH backend and discuss the benefits and limitations of such an approach. As a result, we will also outline the roadmap for supporting ‘delegated storage’ within the dCache releases.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2023

Long-term CRISPR locus dynamics and stable host-virus co-existence in subsurface fractured shales

Viruses are the most ubiquitous biological entities on Earth. Even so, elucidating the impact of viruses on microbial communities and associated ecosystem processes often requires identification of unambiguous host-virus linkages-an undeniable challenge in many ecosystems. Subsurface fractured shales present a unique opportunity to first make these strong linkages via spacers in CRISPR-Cas arrays and subsequently reveal complex long-term host-virus dynamics. Here, we sampled two replicated sets of fractured shale wells for nearly 800 days, resulting in 78 metagenomes from temporal sampling of six wells in the Denver-Julesburg Basin (Colorado, USA). At the community level, there was strong evidence for CRISPR-Cas defense systems being used through time and likely in response to viral interactions. Within our host genomes, represented by 202 unique MAGs, we also saw that CRISPR-Cas systems were widely encoded. Together, spacers from host CRISPR loci facilitated 2,110 CRISPR-based viral linkages across 90 host MAGs spanning 25 phyla. We observed less redundancy in host-viral linkages and fewer spacers associated with hosts from the older, more established wells, possibly reflecting enrichment of more beneficial spacers through time. Leveraging temporal patterns of host-virus linkages across differing well ages, we report how host-virus co-existence dynamics develop and converge through time, possibly reflecting selection for viruses that can evade host CRISPR-Cas systems. Together, our findings shed light on the complexities of host-virus interactions as well as long-term dynamics of CRISPR-Cas defense among diverse microbial populations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Soil Microbes Trade-Off Biogeochemical Cycling for Stress Tolerance Traits in Response to Year-Round Climate Change

Winter air temperatures are rising faster than summer air temperatures in high-latitude forests, increasing the frequency of soil freeze/thaw events in winter. To determine how climate warming and soil freeze/thaw cycles affect soil microbial communities and the ecosystem processes they drive, we leveraged the Climate Change across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest in the northeastern United States, where replicate field plots receive one of three climate treatments: warming (+5°C above ambient in the growing season), warming in the growing season + winter freeze/thaw cycles (+5°C above ambient +4 freeze/thaw cycles during winter), and no treatment. Soil samples were taken from plots at six time points throughout the growing season and subjected to amplicon (rDNA) and metagenome sequencing. We found that soil fungal and bacterial community composition were affected by changes in soil temperature, where the taxonomic composition of microbial communities shifted more with the combination of growing-season warming and increased frequency of soil freeze/thaw cycles in winter than with warming alone. Warming increased the relative abundance of brown rot fungi and plant pathogens but decreased that of arbuscular mycorrhizal fungi, all of which recovered under combined growing-season warming and soil freeze/thaw cycles in winter. The abundance of animal parasites increased significantly under combined warming and freeze/thaw cycles. We also found that warming and soil freeze/thaw cycles suppressed bacterial taxa with the genetic potential for carbon (i.e., cellulose) decomposition and soil nitrogen cycling, such as N fixation and the final steps of denitrification. These new soil communities had higher genetic capacity for stress tolerance and lower genetic capacity to grow or reproduce, relative to the communities exposed to warming in the growing season alone. Our observations suggest that initial suppression of biogeochemical cycling with year-round climate change may be linked to the emergence of taxa that trade-off growth for stress tolerance traits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Argonne Leadership Computing Facility: 2021 Operational Assessment Report

This Operational Assessment Report describes how the Argonne Leadership Computing Facility (ALCF) met or exceeded every one of its goals for calendar year (CY) 2021 as an advanced scientific computing center. In CY 2021, the ALCF operated its production resource, Theta, an Intel-based Cray XC40 system (11.7-petaflops) augmented with 24 NVIDIA DGX A100-based nodes (3.9-petaflops) that supports diverse workloads, integrating data analytics with artificial intelligence (AI) training and learning in a single platform. In 2021, we began deploying Polaris, our newest 40- petaflops system, and augmented this powerful testbed system with an additional 28 nodes to support the integration of real-time experiments and HPC resources. We also deployed our two largest storage systems yet, named Grand and Eagle, that will bring new services to our users and will power data-driven research for years to come. Last year, Theta delivered a total of 20.8 million node-hours to 16 Innovative and Novel Computational Impact on Theory and Experiment (INCITE) projects and 7.2 million node-hours to ASCR Leadership Computing Challenge (ALCC) projects (32 awarded during the 2020–2021 ALCC year and 17 awarded during the 2021–2022 ALCC year), as well as substantial support to Director’s Discretionary (DD) projects (5.5 million node-hours). As Table ES.1 shows, Theta performed exceptionally well in terms of overall availability (95.1 percent), scheduled availability (99.4 percent), and utilization (98.1 percent; Table 2.1). As of the submission date of this document, ALCF’s user community has published 249 papers in high-quality, peer-reviewed journals and technical proceedings. At the 2021 International Conference for High Performance Computing, Networking, Storage and Analysis (SC’21), Argonne researchers won two HPCwire Readers’ Choice Awards and were part of a Gordon Bell Prize finalist team recognized for developing an AI-enabled, multi-resolution simulation framework for studying complex biomolecular machines. Their framework was used to observe the SARS-CoV-2 replication-transcription machinery in action, by directly integrating experimental data. ALCF also provided a comprehensive program of high-performance computing (HPC) support services to help our community make productive use of the facility’s diverse and growing collection of resources. We are now entering the exascale era, with exascale machines being planned for national laboratories across the country, including Aurora at Argonne National Laboratory (Argonne) in 2023. ALCF researchers have been leading and guiding numerous strategic activities that will push the boundaries of what’s possible in computational science and engineering and allow us to deliver science on day one.

97 MATHEMATICS AND COMPUTING↗