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At least 163 records · Page 9

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.

59 BASIC BIOLOGICAL SCIENCES↗

Maps of growing season gross primary production and net ecosystem exchange for Council Road Mile Marker 71, Seward Peninsula, Alaska, [2017-2023]

This data archive is in support of the Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) publication "Integrating Characteristic Arctic Vegetation in a Land Surface Model Improves Representation of Carbon Dynamics Across a Tundra Landscape", by Murphy et al. (2025a). Murphy et al. (2025a) evaluated whether incorporating observed Arctic vegetation heterogeneity into ELM, the land model of the Department of Energy’s Energy Exascale Earth System Model (E3SM), improved simulations of tundra carbon cycling. The associated model archive can be found at Murphy et al. (2025b). The study focused on the spatial patterns and net landscape-level growing season productivity and carbon uptake. As part of this evaluation, observationally derived maps of average growing season (June–August) net ecosystem exchange (NEE) and gross primary production (GPP) were developed for the same domain. These maps, which form the dataset described here, integrate eddy covariance flux tower, remote sensing, and vegetation community data to provide spatially explicit benchmarks for model evaluation. The maps provide spatially explicit estimates of average growing season NEE and GPP across 13 tundra vegetation communities within the study domain. By combining flux tower observations with Airborne Visible-Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG) hyperspectral imagery and drone-based normalized difference vegetation index (NDVI), these maps capture the heterogeneity of carbon fluxes associated with different Arctic vegetation types. While they represent average seasonal conditions rather than interannual variability, the maps provide a unique dataset for evaluating model performance, comparing vegetation community contributions to landscape-scale carbon cycling, and supporting regional analyses of Arctic carbon dynamics. This data archive contains 5 m resolution maps of vegetation communities, vegetation community average growing season GPP, and vegetation community average growing season NEE (three *.tif files), a User’s Guide (*pdf file), and Table 1 of the User’s Guide displaying vegetation community coverage and average growing season NEE and GPP values (*.csv file).

Murphy, Bailey [ORNL] (ORCID:0000000203995221)↗

Passive cooling designs to improve heat resilience of homes in underserved and vulnerable communities

Disadvantaged communities face a growing threat to staying safe during heat waves, especially during coincident power outages. This study develops a methodology to evaluate the effectiveness of passive cooling measures (those that operate without power) to improve residential building heat resilience. Building performance is simulated for representative homes and on district scales in two disadvantaged communities in Fresno, California. Eleven passive measures are evaluated using four heat resilience metrics with and without grid power. Results show performance of the mitigation measures varies by building characteristics, surrounding environment, and power scenario. The two most effective measures were installing solar-control window films and adding roof insulation. For pre-1978 single-family homes, these two measures can reduce unmet degree-hours (UDH) indoors by 12% and 11% respectively without grid power, or 28% and 37% with grid power. Their respective UDH reductions at district scale typically range 8% — 20% and 4% — 12% without grid power, or 14% — 44% and 8% — 51% with grid power. Top floors have higher overheating risk than lower floors during extreme heat events with coincident power outages. Natural ventilation can help, reducing UDH by 21% — 26%. The methodology and findings from this study can help cities, communities, and utilities develop effective and targeted strategies to promote greater residential heat resilience.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Seasonality regulates the structure and biogeochemical impact of ectomycorrhizal fungal communities across environmentally divergent neotropical dry forests

Abstract Ectomycorrhizal (ECM) symbioses support forest functioning globally, yet both the structure and function of ECM fungal communities in seasonally dry neotropical forests (SDTFs), known for extreme heterogeneity in vegetation and edaphic properties, remain under characterized. Here, we evaluated the relative influences of seasonal versus spatial variation in ECM fungal community structure in soils from four environmentally divergent SDTFs. We also assessed the importance of biotic and abiotic drivers of SDTF ECM fungal community structure at regional scales, as well as ECM impacts on soil carbon (C) and nitrogen (N) cycling. ECM fungal frequency, relative abundance and richness all increased in the wet season, but spatial rather than seasonal effects explained more variation in community composition. Across the four SDTFs investigated, differences in tree communities drove ECM fungal community turnover more than geographic distances, site abiotic conditions or soil chemistry. Although soil moisture and ECM tree basal area were stronger predictors of soil biogeochemistry, incorporating ECM fungal community composition and relative abundance added explanatory power to models of soil C and N cycling in the wet season. Synthesis : Our results highlight the importance of seasonality and plant community composition in shaping different aspects of SDTF ECM fungal community structure and diversity as well as the potential for both the plant and fungal components of ECM symbioses to impact soil functioning across heterogenous SDTFs. Furthermore, our findings suggest that alterations in SDTF plant community composition due to climate or land‐use change will have important consequences for ECM fungal diversity and associated effects on soil biogeochemical cycling.

54 ENVIRONMENTAL SCIENCES↗

How deep should we go to understand roots at the top of the world?

Harsh environmental conditions and the short summers of northern, high-latitude biomes impose unique constraints on the plants that live in the arctic tundra and the boreal forest. To escape the harsh aboveground environment, plants in these habitats often allocate a large portion of their biomass belowground to facilitate nutrient acquisition. In turn, the proximity of living plant roots to vast stores of sequestered soil carbon in these biomes means that shifts in rooting depth distribution and the size of the root–soil interface could significantly contribute to ongoing climate change. Indeed, plant ‘priming’ of rhizosphere decomposition via root exudation, particularly from shallowly distributed roots, can lead to losses of carbon from tundra soils. While we have a hard-won understanding of the distribution of plant communities across the arctic tundra and the boreal forest from direct field observations scaled to the landscape level using climate-informed mapping techniques (i.e. the Circumpolar Arctic Vegetation Map (CAVM); Walker et al. , 2005), these vegetation maps are only the tip of the iceberg (Iversen et al. , 2015). Root form and function remain hidden beneath the land surface. In an article recently published in New Phytologist , Blume-Werry et al. (2023, 10.1111/nph.18998) asked whether rooting depth distribution, and ensuing carbon emissions, could be inferred from commonly used vegetation mapping classifications across the pan-Arctic. An important question to guide our understanding, mapping, and prediction of belowground characteristics and ecosystem feedbacks at the top of the world. Unfortunately, they found that the answer was ‘not quite’. While rooting depth distribution varied demonstrably, in turn causing substantial changes in modeled carbon emissions via rhizosphere ‘priming’, variation across rooting depth profiles did not correspond with vegetation mapping classes. If we are unable to predict belowground rooting depth distributions across large spatial scales by leveraging aboveground vegetation community distributions, how then should belowground researchers proceed?

59 BASIC BIOLOGICAL SCIENCES↗

The Compelling Need for a Mid-Scale Stellarator Facility

In the pursuit of the goal of commercial fusion as an abundant and safe source of energy, the stellarator is a leading concept with compelling attractiveness and demonstrated performance. In this white paper we, as a community of US researchers from Universities, National Laboratories, and Private Industry, involved in studying the stellarator concept, lay out the programmatic and technical motivation for a new mid-size stellarator research facility in the US. This contribution is complementary to several other whitepapers authored by members of our community which address different mid-scale stellarator aspects. A community based technical facility proposal has been prepared by F. Parra, et al: Flexible Stellarator Physics Facility. Two private stellarator companies have submitted proposals supporting the development of a mid-scale stellarator: Thea Energy (C.P.S. Swanson, et al.), Type One Energy (W. Guttenfelder, et al.).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

FACETS Dynamical Downscaling Simulations over North America by the CAM-MPAS Variable-Resolution Model

Comprehensive assessment of climate datasets created by statistical or dynamical models is important for effectively communicating model projection and associated uncertainty to stakeholders and decision-makers. The Department of Energy FACETS project aims to foster such communication through development of metrics and their demonstration on a hierarchy of downscaled climate datasets to quantify aspects of climate change projections that are credible, particularly for supporting decisions related to the energy-water-land nexus. As a part of this effort, we have produced a regional climate dataset using the Model for Prediction Across Scales coupled to the Community Atmosphere Model (CAM-MPAS). This global modeling framework is configured with variable-resolution meshes featuring higher resolutions over North America, as well as quasi-uniform resolution meshes across the globe. The variable-resolution configurations allow fine-scale features to be better resolved inside the refinement and interact with global-scale circulations. The dataset includes multiple uniform- (240km and 120km) and variable-resolution (200-50km, 100-25km, and 46-12km) simulations that are designed to be compatible with other regional climate simulations that contribute to the hierarchy of downscaled climate datasets of the project. Furthermore, the dataset consists of simulations for both the present-day (1989-2010) and future (2079-2100) climate and post-processing of the model output has been coordinated across the project for consistency to facilitate common analysis across the hierarchy of datasets. Altogether, this CAM-MPAS model dataset provides a unique opportunity to assess the influence of resolutions and modeling framework on model credibility and climate change projection.

Sakaguchi, Koichi↗

A building performance-based approach to determining energy resilience for grocery stores in the event of a power outage

Evaluating progress toward a built environment that is best equipped to serve communities during a regional power outage will require metrics that capture the energy resilience of the unique buildings and businesses most crucial to the well-being of those nearby. We focused on grocery stores as key buildings for which access, and thus energy resilience, is critical during a disaster when power is unavailable. We evaluated the energy resilience of these buildings by offering and testing building-scale metrics that assess business continuity potential during a power outage. Metrics proposed in this study are calculated based on the unique power loads characteristic to grocery stores, primarily refrigeration and maintaining safe indoor environmental conditions. Building simulations based on varying levels of backup power were carried out against occupant safety and comfort parameters to apply these metrics, with additional criteria imposed on grocery stores to capture the inventory and sales loss from food spoilage resulting from a lack of refrigeration power. Findings from this study demonstrate the feasibility of our proposed metrics and methodology to serve as a low-data burden means for stakeholders to evaluate the energy resilience of grocery stores, with greater implications in helping to understand the impact on community-scale energy resilience.

Siegel, Lino Sanchez↗

Using National-Scale Data to Inform Coal Power Plant Redevelopment and Coal Community Revitalization Planning

In the United States, individual coal plants have high variation in their construction and operation. Coal plants commonly have multiple units, with different commissioning ages, operational position, and maintenance conditions – even multiple fuels. These units may be in changing states of utilization, with variation in productivity depending on economic contexts. Coal plants themselves may be temporarily offline, mothballed, retired, or decommissioned due to owner/operator portfolios or market conditions, and the current posture of the plant may be difficult to ascertain without local news sources (Tarekegne et al. 2021). Anticipated dates of plant closures are prospectively represented to regulators and to the Energy Information Administration (EIA), but may also experience uncertainty due to the engineering, environmental, economic and social complexity of closing a very large power plant. As noted in this report, closure of the first unit to the last within a single plant may span more than 20 years. Yet tracking and predicting the position of our nation’s coal fleets on a national scale is deeply important. In developing a case for federal datasets and an approach to building and curating these data, this report identified that data must have high fidelity at the plant-level to be meaningful in aggregate. Plant-scale detail is also a match for its application: national priorities in federal investment range from economic revitalization for coal plant communities to maintaining reliable electric grid operations. This document is organized into a statistical review of coal plant retirements, past and prospective, in the United States; trends in the relationship between closures and existing federal investment programs for community revitalization; and potential methods for accelerating site redevelopment through advanced geospatial analysis based on federal data.

01 COAL, LIGNITE, AND PEAT↗

Evaluation of DNA Extraction Efficiency in Diverse Algae Strains Using Commercial Kits and Lysis Approaches

Efficient DNA extraction is essential for accurately monitoring microalgae communities in large-scale cultivation systems such as raceway ponds and wastewater ponds. Traditional phenol chloroform extracts are a staple in microbiology but are obsolete for routine sampling due to its high toxicity reagents and time intensive setups. Commercial DNA extraction kits are more favorable for the microbes found in these ponds, but lack specific kits made for these communities. Little is known about which kits perform the best, leading researchers to use a variety of different kits with inconsistent results. This project compared one precipitation based commercial kit (Lucigen Masterpure) and five wash based kits (Monarch, Zymo Quick-DNA, and three Qiagen DNeasy kits) using four brackish algae strains to determine which methods yield the greatest quantity and quality of genomic DNA. Extractions were evaluated using the manufacturers protocol, and additional pretreatment options were administered before a single kit to compare its potential in being added routinely before extractions. Pretreatment options included both cryogenic freeze-thawing and heat incubation using enzymes. DNA was quantified using Qubit fluorometry and NanoDrop purity ratios. Overall, the Qiagen PowerWater kit provided the highest DNA yield and purity, but at a significantly higher cost then the precipitation-based kit (MasterPure). It was also noted that while the precipitation-based kit was significantly cheaper, provided similar results, it took significantly more time to complete a single run. Cryogenic pretreatment (6x cycles) increased average DNA yields by up to 80%, whereas enzymatic pretreatment most improved purity ratios without substantially improving quantity. The results suggest that it may be more cost and time efficient to use Qiagen kits with the addition of lysis pretreatments to procure better results. Future works includes developing a better system to efficiently collect multi variable data, and to upscale to artificial polycultures using similar methodologies alongside sequencing to confirm kit results.

59 BASIC BIOLOGICAL SCIENCES↗

Sizing Small-Scale Renewable Energy Systems for the Navajo Nation and Rural Communities

The Navajo Nation consists of about 55,000 residential homes spread across 27,000 square miles of trust land in the Southwest region of the United States. The Navajo Tribal Utility Authority (NTUA) reports that approximately 15,000 homes on the reservation do not have electricity due to the high costs of connecting rural homes located miles from utility distribution lines. In order to get these rural homeowners access electricity, NTUA and other Native owned companies are examining small-scale renewable energy systems to provide power for necessary usage such as lighting and refrigeration. The goal of this study is to evaluate the current renewable deployment efforts and provide additional considerations for photovoltaic (PV) systems that will optimize performance and improve efficiency to reduce costs. There are three case studies presented in different locations on the Navajo Nation with varying solar resource and energy load requirements. For each location, an assessment is completed that includes environmental parameters of the site- specific landscape and a system performance analysis of an off-grid residential PV system. The technical process, repeated for each location, demonstrates how the variance and uniqueness of each household can impact the system requirements after optimizations are applied. Therefore, the household variabilities and difference in locations must be considered. The differing results of each case study suggests additional analysis is needed for designing small-scale PV systems that takes a home-land-family specific approach to allow for better efficiency and more flexibility for future solar innovations to be considered for overall cost reductions.

14 SOLAR ENERGY↗

Environmental harshness mediates the relationship between aboveground and belowground communities in Antarctica

Linkages between aboveground and belowground communities are a key but globally under-researched component of responses to environmental change. Given the logistical complications to studying these relationships, much of our knowledge derives from laboratory experiments and localized field studies which have so far yielded inconsistent results. Because environmental factors may alter relationships between above- and belowground communities, there is a need for broad-scale field studies testing these interactions. The Antarctic Peninsula provides an ideal test setting, given the relatively simple communities both above- and belowground. The Peninsula is also experiencing rapid environmental changes, including alterations in species diversity and distribution both above- and belowground. Thus, an improved understanding of the broad-scale consequences of altered environments and vegetation communities for the soil microbiome is of high priority. To determine the nature and strength of the relationship between in situ plant and soil communities across a broad spatial scale and range of environmental conditions, we sampled soil communities at 9 locations (spanning 60–72°S along the Scotia Arc and Antarctic Peninsula) beneath the major aboveground habitats (moss, grass, lichen, algae and bare soil). We measured a comprehensive suite of soil physicochemical properties, microbial (bacterial and fungal) diversity and composition, and invertebrate abundance and community composition to determine the relationships between plant and soil communities. Furthermore, our results suggest that, with increased environmental severity, plant cover types become more important for influencing the physicochemical soil environment, and therefore the soil microbial communities. Although we found site-specific relationships, broad-scale patterns reveal significant differences among bare soils and vegetated soils, particularly soils beneath grass and moss. This suggests that expansion of vegetation communities under current climate warming projections will be accompanied by shifts in the soil microbiome, with important implications for the ecosystem functioning with which they are associated.

54 ENVIRONMENTAL SCIENCES↗

Multi-scale Simulation, Calibration, and Optimization of Calcium Carbonate Precipitation in Microbial Communities

Ensuring the efficient engineering of microbially induced calcium carbonate precipitation (MICP) is crucial for a variety of environmental and civil engineering applications, such as soil stabilization and carbon sequestration. Addressing this need, we present a comprehensive multi-scale workflow that begins with the isolation of calcium carbonate-producing microbes from soil samples, followed by metagenomic sequencing and metabolic reconstruction. We then characterize microbial growth phenotypes under diverse nutrient conditions, compare observed growth with metabolic model predictions, and apply the Consistent Reproduction of Phenotype (CROP) algorithm to refine these models. Furthermore, we analyze metabolite consumption and production, and develop a consumer-resource model that is calibrated using time-series measurements of growth rates, pH levels, and calcium carbonate precipitation. The primary benefit of our approach lies in its ability to predict and control MICP outcomes, facilitated by a Bayesian methodology that incorporates priors on initial conditions and parameters. This allows us to compute posteriors by integrating experimental data, and to solve a risk optimization problem under uncertainty to identify nutrient conditions that maximize calcium carbonate production. In contrast to non-Bayesian methods, which fail to quantify uncertainty accurately, our approach provides a more reliable pathway to optimizing nutrient conditions, enhancing the likelihood of achieving desired MICP outcomes. This positions our method as a superior alternative in the quest to improve MICP through engineered microbial consortia.

54 ENVIRONMENTAL SCIENCES↗

Examining Tropical Convection Features at Storm-Resolving Scales Over the Maritime Continent Region

Global Storm Resolving Models (GSRMs) provide a way to understand weather and climate events across scales for better-informed climate impacts. In this work, we apply the recently developed and validated CAM (Community Atmosphere Model)—MPAS (Model for Prediction Across Scales) modeling framework, based on the open-source Community Earth System Model (CESM2), to examine the tropical convection features at the storm resolving scale over the Maritime Continent region at 3 km horizontal spacing. We target two global numerical experiments during the winter season of 2018 for comparison with observation in the region. Here we focus on the investigation of the representations of the convective systems, precipitation statistics, and tropical cyclone behaviors. We found that regional-refined experiments show more accurate precipitation distributions, diurnal cycles, and better agreement with observations for tropical cyclone features in terms of intensity and strength statistics. We expect the exploration of this work will further advance the development and use of the storm-resolving model in precipitation predictions across scales.

54 ENVIRONMENTAL SCIENCES↗

Best Practices for Equitable Solar Workforce Development

The Midwest Renewable Energy Association (MREA) was selected to serve as a lead organization for the U.S. Department of Energy Solar Energy Technology Office’s Equitable Solar Communities of Practice initiative. This project, facilitated through a partnership with ENERGYWERX, aimed to develop strategies to support the expansion of equitable benefits in solar adoption across the U.S. Specifically, the MREA was chosen to lead the solar workforce development community of practice, focusing on scaling the U.S. solar workforce, to meet growing industry demands and ensure that these opportunities are accessible and beneficial to all communities. For the purpose of this initiative, we define the solar workforce in line with the National Solar Jobs Census, which defines a solar worker as someone who spends a majority of their time on solar-related work. This also includes workers who spend a plurality of their time on solar tasks. It’s important to note that manufacturing jobs were not included in this research, as the focus is primarily on solar installation, development, and related roles. To achieve the goals of the Equitable Solar Communities of Practice initiative, the MREA leveraged existing resources and engaged a diverse core team and group of stakeholders including industry professionals, educators, policymakers, and community leaders. The MREA began with a literature review and gap analysis to identify existing best practices and gaps in the solar workforce. This was followed by a community convening to gather insights from a wide range of stakeholders. The findings informed the best practices and pathways to scale the benefits of solar workforce development, focusing on training programs, workforce services, apprenticeship, and justice, inclusion, and sustainability. This report outlines the background, methodology, findings, and conclusions drawn from the landscape and gap analysis, providing valuable insights into workforce needs and training program capacities across the U.S. The outcomes of this research are presented in this report and contain recommendations for optimizing workforce development and training funding to support the equitable growth of the solar industry, ensuring that the transition to solar energy is inclusive and beneficial for all communities.

14 SOLAR ENERGY↗

Rapid Open-Air Processing of Low-Cost Perovskite Solar Modules

We report an industrially relevant approach to both scalable and fast open-air perovskite photovoltaic (PV) module production. This work resolves some of the most formidable barriers to module-level scaling that the perovskite community has been facing. Key advances include scalable large-area spray deposition, new monolithic integration scribing techniques, advanced photoluminescence characterization, and reproducible high-throughput manufacturability. Our rapid spray processing techniques enabled the highest perovskite PV efficiency produced in open-air. Innovations in scribing techniques enabled the first single-source laser process to achieve perovskite module monolithic integration and technoeconomic analysis led to a comprehensive cost model for perovskite module manufacturing. We report significant progress in reducing perovskite manufacturing costs necessary to potentially compete with incumbent Si-based PV for utility-scale power generation.

cost modeling↗

Network structure of vertebrate scavenger assemblages at the global scale: drivers and ecosystem functioning implications

The organization of ecological assemblages has important implications for ecosystem functioning, but little is known about how scavenger communities organize at the global scale. Here, we test four hypotheses on the factors affecting the network structure of terrestrial vertebrate scavenger assemblages and its implications on ecosystem functioning. We expect scavenger assemblages to be more nested (i.e. structured): 1) in species-rich and productive regions, as nestedness has been linked to high competition for carrion resources, and 2) regions with low human impact, because the most efficient carrion consumers that promote nestedness are large vertebrate scavengers, which are especially sensitive to human persecution. 3) We also expect climatic conditions to affect assemblage structure, because some scavenger assemblages have been shown to be more nested in colder months. Finally, 4) we expect more organized assemblages to be more efficient in the consumption of the resource. We first analyzed the relationship between the nestedness of the scavenger assemblages and climatic variables (i.e. temperature, precipitation, temperature variability and precipitation variability), ecosystem productivity and biomass (i.e. NDVI) and degree of human impact (i.e. human footprint) using 53 study sites in 22 countries across five continents. Then, we related structure (i.e. nestedness) with its function (i.e. carrion consumption rate). We found a more nested structure for scavenger assemblages in regions with higher NDVI values and lower human footprint. Moreover, more organized assemblages were more efficient in the consumption of carrion. However, our results did not support the prediction that the structure of the scavenger assemblages is directly related to climate. Our findings suggest that the nested structure of vertebrate scavenger assemblages affects its functionality and is driven by anthropogenic disturbance and ecosystem productivity worldwide. Disarray of scavenger assemblage structure by anthropogenic disturbance may lead to decreases in functionality of the terrestrial ecosystems via loss of key species and trophic facilitation processes.

54 ENVIRONMENTAL SCIENCES↗