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At least 811 records · Page 45

Trend Detection of Atmospheric Time Series: Incorporating Appropriate Uncertainty Estimates and Handling Extreme Events

This paper is aimed at atmospheric scientists without formal training in statistical theory. Its goal is to, 1) provide a critical review of the rationale for trend analysis of the time series typically encountered in the field of atmospheric chemistry; 2) describe a range of trend-detection methods; and 3) demonstrate effective means of conveying the results to a general audience. Trend detections in atmospheric chemical composition data are often challenged by a variety of sources of uncertainty, which often behave differently to other environmental phenomena such as temperature, precipitation rate, or stream flow, and may require specific methods depending on the science questions to be addressed. Some sources of uncertainty can be explicitly included in the model specification, such as autocorrelation and seasonality, but some inherent uncertainties are difficult to quantify, such as data heterogeneity and measurement uncertainty due to the combined effect of short- and long-term natural variability, instrumental stability, and aggregation of data from sparse sampling frequency. Failure to account for these uncertainties might result in an inappropriate inference of the trends and their estimation errors. On the other hand, the variation in extreme events might be interesting for different scientific questions, for example, the frequency of extremely high surface ozone events and their relevance to human health. In this study we aim to, 1) review trend detection methods for addressing different levels of data complexity in different chemical species; 2) demonstrate that the incorporation of scientifically interpretable covariates can outperform pure numerical curve fitting techniques in terms of uncertainty reduction and improved predictability; 3) illustrate the study of trends based on extreme quantiles that can provide insight beyond standard mean or median based trend estimates; and 4) present an advanced method of quantifying regional trends based on the inter-site correlations of multi-site data. All demonstrations are based on time series of observed trace gases relevant to atmospheric chemistry, but the methods can be applied to other environmental data sets.

Trace gas↗

A Thermodynamic Paradigm for Studying Disease Vector’s Habitats & Life Cycles Using NASA’s NextGen Remote Sensing Instruments

Global public health is entering a new informational age through the use of spatial models of disease vector/host ecologies driven by the use of remotely sensed data to measure environmental and structural factors critical in determining disease vector habitats, distributions, life cycles, and host interactions. The vector habitat microclimates can be quantified in terms of the surface energy budget measured by satellites. The epidemiological equations (processes) can be adapted and modified to explicitly incorporate environmental factors and interfaces required by a specific disease and its vector/host cycle. Remote sensing can be used to measure or evaluate or estimate both environment (state functions) and interface (process functions). Remote sensing can be used to measure or evaluate or estimate both environment (state functions) and interface (process functions) defining vector habitats. The products of remote sensing can be integrated directly into the epidemiological equations to significantly enhance our understanding of disease vector’s life cycles and habitats. The next generation of NASA’s remote sensing instruments recently operational will provide a significant enhancement in our ability to study disease vector’s life cycles and habitats. Three new instruments have become operational on the International Space Station (ISS) In June 2018, ECOSTRESS (The ECOsystem Spaceborne Thermal Radiometer Experiment on Space Station), a five channel, thermal IR instrument with 70 m resolution and approximately 4-5 day repeat cycle of day/night pairs along with DESISa hyperspectral sensor system 235 channels (between 400 and 1000 nanometers), 30 m resolution, and data only being acquired on demand. In November 2018. GEDI (Global Ecosystem Dynamics Investigation). GEDI is a high-resolution laser ranging of Earth’s forests and topography. These instruments set the stage for NASA’s new global designated observables set of remote sensing measurements collecting hyperspectral and multispectral thermal data called SBG (Surface Biology Geology). The SBG is currently in the planning stage. The availability and use of level 1-4 data products generated from these ISS instruments will be discussed.

thermodynamics↗

Combining Modis and Quikscat Data to Delineate Surface and Near-Surface Melt on the Greenland Ice Sheet

Over the last two decades, increasing melt has been measured on the Greenland Ice Sheet, along with mass loss as determined from satellite data, Monitoring the state of the Greenland Ice Sheet becomes critical especially because it is actively losing mass, and the ice sheet has a sea-level rise potential of 7 in. However measurement of the extent of surface melt varies depending on the sensor used, whether it is passive or active microwave or visible or thermal infrared. We have used remote-sensing data products to study surface and near-surface melt characteristics of the Greenland Ice Sheet. We present a blended MODIS-QS melt daily product for 2007 [1]. The products, including Moderate Resolution Imaging Spectroradiometer (MODIS) daily land-surface temperature (LST) and a special daily melt product derived from the QuikSCAT (QS) scatterometer [2,3] show consistency in delineating the melt boundaries on a daily basis in the 2007 melt season [I], though some differences are identified. An assessment of maximum melt area for the 2007 melt shows that the QSCAT product detects a greater amount of melt (862,769 square kilometers) than is detected by the MODIS LST product (766,184 square kilometers). The discrepancy is largely because the QS product can detect both surface and near-surface melt and the QS product captures melt if it occurred anytime during the day while the MODIS product is obtained from a point in time on a given day. However on a daily bases, other factors influence the measurement of melt extent. In this work we employ the digital-elevation model of Bamber et al. [4] along with the National Centers for Environmental Prediction (NCEP) data to study some areas and time periods in detail during the 2007 melt season. We focus on times in which the QS and MODIS LST products do not agree exactly. We use NCEP and elevation data to analyze the atmospheric factors forcing the melt process, to gain an improved understanding of the conditions that lead to melt and melt persistence, and our ability to capture surface melt accurately using MODIS and QS data.

Hall, Dorothy K.↗

Harnessing: Technologies for Sustainable Reindeer Husbandry in the Arctic

To accelerate the development of sustainable reindeer husbandry under the lead of indigenous reindeer herders, it is critical to empower reindeer herders with the best available technologies and to promote a new kind of science where traditional knowledge is fully integrated into the scientific management of the natural environment in the Arctic. This is particularly true given the dramatic environmental, climatic, economic, social and industrial changes, which have taken place across the Arctic in recent years, all of which have had serious impacts on the reindeer herding communities of the North. The Anar Declaration, adopted by the 2d World Reindeer Herders Congress (WRHC), in Inari, Finland, June 2001drew guidelines for the development of a sustainable reindeer husbandry based on reindeer peoples values and goals. The declaration calls for the reindeer herding peoples to be given the possibilities to develop and influence the management of the reindeer industry and its natural environment because of their knowledge and traditional practices. At the same time, Arctic scientists from many institutions and governments are carrying out increasingly highly technical reindeer related research activities. It is important that the technologies and results of these activities be more commonly co-produced with the reindeer herder community and/or made more readily available to the reindeer peoples for comparison with traditional knowledge for improved herd management. This paper describes a project in which reindeer herders and scientists are utilizing technologies to create a system for collecting and sharing knowledge. The project, Reindeer Mapper, is creating an information management and knowledge sharing system, which will help make technologies more readily available to the herder community for observing, data collection and analysis, monitoring, sharing, communications, and dissemination of information - to be integrated with traditional, local knowledge. The paper describes some of the technologies which comprise the system including an intranet system to enable the team members to work together and share information electronically, remote sensing data for monitoring environmental parameters important to reindeer husbandry (e.g. SAR, Landsat), acquisition of ground-based measurements, and the GIS-based information management and knowledge sharing system.

Maynard, Nancy G.↗

Current and future federal and state sampling guidance for per- and polyfluoroalkyl substances in environmental matrices

Per- and polyfluoroalkyl substances (PFAS) are a class of emerging contaminants composed of an estimated 5000 to 10,000 human-made, fluorinated, organic chemicals. Due to the complexity of PFAS, the need for multiple environmental matrix considerations and the absence of a promulgated federal standard for environmental sampling and analysis, U.S. states have begun developing health-based regulatory and/or guidance values for a limited number of PFAS in environmental matrices. As there is a growing body of science to inform PFAS sampling guidance standard development, it is important to understand which U.S. states are implementing sampling guidelines and how they plan to handle emerging PFAS. This critical review discusses the current and impending federal and state sampling guidelines for PFAS in environmental matrices, the data gaps surrounding PFAS sampling guidance in U.S. states, and the future impacts of impending guidance documents and regulations. Ten federal guidance documents are available for PFAS sampling guidance and analysis. The maximum number of PFAS covered in these guidance documents is 25 analytes spanning across 8 unique media. While the EPA has developed several different sampling and analytical guidelines for PFAS, there is no formal regulation of PFAS or requirements of states to enforce these guidelines. Consequently, only 31 states have informally adopted sampling guidelines, while the other 19 states have no guidance documentation in place for PFAS. The introduction of new PFAS sampling guidelines by the EPA, as well as updated analytical guidelines that target more PFAS or total organofluoride, is expected to continuously shift the landscape of federal and state guidance for PFAS sampling moving forward.

54 ENVIRONMENTAL SCIENCES↗

Effects of Long Duration Space Flight on Low Frequency Hearing

Pure tone hearing threshold data has been collected on astronauts since the early days of spaceflight. Between 1981 and 2001 (STS-1 thru 108) it was found that of the 608 shuttle astronauts, 17% returned home with a significant hearing threshold shift, and of that 6% had permanent changes in the high frequencies. Believed to be due to prolonged noise exposure on the space crafts. (Hart, 2006) As NASA aimed for longer duration missions the uncertainty about the effects of month-long noise exposure needed to be addressed. To avoid constraining crewmembers to constant earplug usage, and satisfying budget demands, a focused effort on overcoming the issues began. Noise monitoring systems were introduced onto the International Space Station (ISS) and astronauts were given education on the noise environment aboard the ISS, the hazards of noise induced hearing loss, hearing conservation principles, and countermeasure strategies (earplugs, noise cancellation headsets). As well as being trained on a new countermeasure effort that had been in trial testing on prior shuttle missions (STS-6 thru 8), On-Orbit Hearing Assessment (OOHA). (Hart, 2006) OOHA was implemented to routinely monitor the hearing thresholds of crewmembers who are on orbit for longer than 30 days. Flight Surgeons on ground monitor these test for significant hearing changes while aboard. Between 2000 and 2021 the ISS OOHA system (EarQ) recorded changes in the low frequency hearing thresholds. Low frequency hearing changes are not typically caused by noise exposure, and it was initially believed that these changes were due to environmental noise interference. In 2021 an ISS software upgrade (KUDUwave) allowed for a more comprehensive hearing assessment. The new testing system allowed for additional tests that helped describe the type of hearing loss being experienced and determine the influence of ambient noise or other environmental factors. OOHA Data indicates a low frequency hearing shift in 40% of all tests and 60% of all crewmembers. Since 2021, OOHA results (using the KUDUwave) suggest that these shifts are sensorineural and are not the result of ambient noise. While hearing shifts are seen at both 250 and 500 Hz, metrics tracking these shifts have only used 500 Hz data. The lack of 250 Hz has prevented accurate reporting of low frequency hearing shift recovery. The aim of this study is to capture 250 Hz data and accurately present low frequency hearing loss recovery.

hearing↗

Nuclear Safety [Vol. 29, No. 3, July-September 1988]

Nuclear Safety is a review journal that covers significant developments in the field of nuclear safety. Its scope includes the analysis and control of hazards associated with nuclear energy, operations involving fissionable materials, and the products of nuclear fission and their effects on the environment. Primary emphasis is on safety in reactor design, construction, and operation; however, the safety aspects of the entire fuel cycle, including fuel fabrication, spent-fuel processing, nuclear waste disposal, handling of radioisotopes, and environmental effects of these operations, are also treated. Table of Contents for this issue follows. GENERAL SAFETY CONSIDERATIONS: 259 Fifteenth Water Reactor Safety Information Meeting by E. G. Silver; CONTROL AND INSTRUMENTATION: 284 Reliability Technology to Improve and/or Maintain Emergency Diesel Generator Performance by S. Karimian and J. H. Taylor, 293 A Noise Diagnostics System for Operator Advice by G. Hessel, P. Liewers, P. Schumann, W. Schmitt, and F.-P. Weiss; PLANT SAFETY FEATURES: 307 A Passive Containment System for Advanced Light-Water Reactors by O. B. Falls, Jr., and F. W. Kleimola; ENVIRONMENTAL EFFECTS: 318 Data Base Construction for a Computerized Radiological Risk Investigation System by L. M. Hively, J. E. Nyquist, J. L. Bledsoe, and A. L. Sjoreen, 326 Erratum to "Radiation Hormesis and Nuclear Safety," Vol. 29, No. 1; OPERATING EXPERIENCES: 327 Operational Safety Experience and Passive Safety Testing at the Fast Flux Text Facility by Q. L. Baird, J. L. Rathbun, D. D. Stepnewski, R. L. Stover, and A. E. Waltar, 344 Backfilling of Independent Residual Heat Removal Systems in West Germany and Switzerland by G. Eckert and Y. Salomon, 353 Reactor Shutdown Experience Compiled by J. W. Cletcher, 356 Selected Safety-Related Events Compiled by G. A. Murphy, 363 Operating U.S. Power Reactors Compiled by E. G. Silver; RECENT DEVELOPMENTS: 384 General Administrative Activities Compiled by E. G. Silver, 390 Reports, Standards, and Safety Guides by D. S. Queener, 395 Status of Power-Reactor Projects Undergoing Licensing Review Compiled by E. G. Silver, 400 Proposed Rule Changes as of Mar. 31,1988; ANNOUNCEMENTS: 283 International ENS/ANS Conference on Thermal Reactor Safety "NUCSAFE 88", 317 Northwestern University Short Course on Radiation Safety, 407 Second International Seminar on Small- and Medium-Sized Nuclear Reactors, 407 International Workshop on New Developments in Occupational Dose Control and ALARA Implementation at Nuclear Power Plants and Similar Facilities, 408 Fourth International Topical Meeting on Nuclear Reactor Thermal Hydraulics (NURETH-4), 404 The Authors.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Nuclear Safety [Vol. 29, No. 3, July-September 1988]

Nuclear Safety is a review journal that covers significant developments in the field of nuclear safety. Its scope includes the analysis and control of hazards associated with nuclear energy, operations involving fissionable materials, and the products of nuclear fission and their effects on the environment. Primary emphasis is on safety in reactor design, construction, and operation; however, the safety aspects of the entire fuel cycle, including fuel fabrication, spent-fuel processing, nuclear waste disposal, handling of radioisotopes, and environmental effects of these operations, are also treated. Table of Contents for this issue follows. GENERAL SAFETY CONSIDERATIONS: 259 Fifteenth Water Reactor Safety Information Meeting by E. G. Silver; CONTROL AND INSTRUMENTATION: 284 Reliability Technology to Improve and/or Maintain Emergency Diesel Generator Performance by S. Karimian and J. H. Taylor, 293 A Noise Diagnostics System for Operator Advice by G. Hessel, P. Liewers, P. Schumann, W. Schmitt, and F.-P. Weiss; PLANT SAFETY FEATURES: 307 A Passive Containment System for Advanced Light-Water Reactors by O. B. Falls, Jr., and F. W. Kleimola; ENVIRONMENTAL EFFECTS: 318 Data Base Construction for a Computerized Radiological Risk Investigation System by L. M. Hively, J. E. Nyquist, J. L. Bledsoe, and A. L. Sjoreen, 326 Erratum to "Radiation Hormesis and Nuclear Safety," Vol. 29, No. 1; OPERATING EXPERIENCES: 327 Operational Safety Experience and Passive Safety Testing at the Fast Flux Text Facility by Q. L. Baird, J. L. Rathbun, D. D. Stepnewski, R. L. Stover, and A. E. Waltar, 344 Backfilling of Independent Residual Heat Removal Systems in West Germany and Switzerland by G. Eckert and Y. Salomon, 353 Reactor Shutdown Experience Compiled by J. W. Cletcher, 356 Selected Safety-Related Events Compiled by G. A. Murphy, 363 Operating U.S. Power Reactors Compiled by E. G. Silver; RECENT DEVELOPMENTS: 384 General Administrative Activities Compiled by E. G. Silver, 390 Reports, Standards, and Safety Guides by D. S. Queener, 395 Status of Power-Reactor Projects Undergoing Licensing Review Compiled by E. G. Silver, 400 Proposed Rule Changes as of Mar. 31,1988; ANNOUNCEMENTS: 283 International ENS/ANS Conference on Thermal Reactor Safety "NUCSAFE 88", 317 Northwestern University Short Course on Radiation Safety, 407 Second International Seminar on Small- and Medium-Sized Nuclear Reactors, 407 International Workshop on New Developments in Occupational Dose Control and ALARA Implementation at Nuclear Power Plants and Similar Facilities, 408 Fourth International Topical Meeting on Nuclear Reactor Thermal Hydraulics (NURETH-4), 404 The Authors.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Remote sensing and urban public health

The applicability of remote sensing in the form of aerial photography to urban public health problems is examined. Environmental characteristics are analyzed to determine if health differences among areas could be predicted from the visual expression of remote sensing data. The analysis is carried out on a socioeconomic cross-sectional sample of census block groups. Six morbidity and mortality rates are the independent variables while environmental measures from aerial photographs and from the census constitute the two independent variable sets. It is found that environmental data collected by remote sensing are as good as census data in evaluating rates of health outcomes.

Rush, M.↗

Ten questions concerning Large Language Models (LLMs) for building applications

Large Language Models (LLMs) are emerging as powerful AI tools capable of transforming how building information is collected, processed, analyzed, and applied across diverse research areas. Their capabilities can help building operators, facility managers and other stakeholders such as designers, architects and engineers by providing actionable insights for decision-making across planning, construction, operations, and maintenance of buildings and facilities. This paper explores ten key questions concerning the role of LLMs in shaping sustainable, intelligent, and human-centric buildings. From fundamental definitions to advanced applications, we examine how LLMs facilitate decision-making across the life cycle of buildings and energy systems. LLMs can enhance life cycle assessments (LCA), building energy simulations, and real-time data integration, empowering more efficient and adaptive human-AI environments. They can also contribute to streamlining regulatory compliance, improving post-occupancy evaluations, and fostering more inclusive and participatory design processes. Additionally, this paper addresses the ethical challenges posed by LLMs, such as bias, data privacy, and environmental impacts, and explores their potentials in advancing intelligent digital twins (DT) for ongoing building operations and maintenance. Built upon our applied research using LLMs and the review of tools, datasets, and research gaps, we provide a forward-looking perspective on how LLMs can drive innovation, collaboration, and productivity in the built environment while supporting ethical and effective implementation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Sustainable materials acceleration platform reveals stable and efficient wide-bandgap metal halide perovskite alloys

The vast chemical space of emerging semiconductors, like metal halide perovskites, and their varied requirements for semiconductor applications have rendered trial-and-error environmentally unsustainable. Here, in this work, we demonstrate RoboMapper, a materials acceleration platform (MAP), that achieves 10-fold research acceleration by formulating and palletizing semiconductors on a chip, thereby allowing high-throughput (HT) measurements to generate quantitative structure-property relationships (QSPRs) considerably more efficiently and sustainably. We leverage the RoboMapper to construct QSPR maps for the mixed ion FA 1-y Cs y Pb(I 1-x Br x ) 3 halide perovskite in terms of structure, bandgap, and photostability with respect to its composition. We identify wide-bandgap alloys suitable for perovskite-Si hybrid tandem solar cells exhibiting a pure cubic perovskite phase with favorable defect chemistry while achieving superior stability at the target bandgap of ~1.7 eV. RoboMapper’s palletization strategy reduces environmental impacts of data generation in materials research by more than an order of magnitude, paving the way for sustainable data-driven materials research.

36 MATERIALS SCIENCE↗

Statistical Uncertainty in Paleoclimate Proxy Reconstructions

A quantitative analysis of any environment older than the instrumental record relies on proxies. Uncertainties associated with proxy reconstructions are often underestimated, which can lead to artificial conflict between different proxies, and between data and models. In this paper, using ordinary least squares linear regression as a common example, we describe a simple, robust and generalizable method for quantifying uncertainty in proxy reconstructions. We highlight the primary controls on the magnitude of uncertainty, and compare this simple estimate to equivalent estimates from Bayesian, nonparametric and fiducial statistical frameworks. We discuss when it may be possible to reduce uncertainties, and conclude that the unexplained variance in the calibration must always feature in the uncertainty in the reconstruction. This directs future research toward explaining as much of the variance in the calibration data as possible. We also advocate for a “data-forward” approach, that clearly decouples the presentation of proxy data from plausible environmental inferences.

58 GEOSCIENCES↗

MFRED, 10 second interval real and reactive power for groups of 390 US apartments of varying size and vintage

Abstract Building electricity is a major component of global energy use and its environmental impacts. Detailed data on residential electricity use have many interrelated research applications, from energy conservation to non-intrusive load monitoring, energy storage, integration of renewables, and electric vs. fossil-based heating. The dataset presented here, Multifamily Residential Electricity Dataset (MFRED), contains the electricity use of 390 apartments, ranging from studios to four-bedroom units. All apartments are located in the Northeastern United States (IECC-climate-zone 4 A), but differ in their heating/cooling system and construction year (early to late 20 th century). To adhere to privacy guidelines, data were averaged across 15 apartments each, based on annual electricity use. MFRED includes real and reactive power, at 10-second resolution, for January to December 2019 (246 million data points). The annual average real power per apartment is 343 W (3.27 W/m 2 of floor area), with strong variation between seasons and apartment size. Considering its large number of apartments, high time resolution, real and reactive power, and 12-month duration, MFRED is currently unique for the multifamily-sector.

97 MATHEMATICS AND COMPUTING↗

Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface

Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal-contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of the Castellaniella genus concurrent with increased denitrification rates. Thus, we asked how genomic and abiotic factors control the Castellaniella biogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. We report the isolation and characterization of several Castellaniella strains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to two Castellaniella amplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least 2 decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase (nos) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.

59 BASIC BIOLOGICAL SCIENCES↗

Preliminary Assessment of Qiskit Quantum Simulator Capabilities for Development of Quantum Hopfield Neural Network for Anomaly Detection Applications (Q4 Report)

Quantum information processing offers potentially faster performance compared to the classical counterpart. The goal of this work is to investigate performance of Quantum Hopfield Neural Network for applications to anomaly detection. Preliminary study consist of assessment of computational capabilities of Qiskit quantum simulator. Eventual objective is to implement Quantum Hopfield Network algorithm for detection of weak nuisance and anomaly signal in the presence of strong and highly varying background in gamma radiation data measured during environmental screening.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Hidden in Plain Sight: How Interior Furnishings Management Can Help Los Alamos National Laboratory Meet the United States Department of Energy's Sustainability Goals [Capstone Project]

In the last three years, LANL has purchased over $50 million in new interior products with a focus on sustainable building and high-quality interior furnishings, carpet, and paint. Purchasing interior products that focus on sustainable manufacturing, however, is only the beginning of properly operating and maintaining an interior space over its useable life. Sustainable commercial furniture, if well maintained and warrantied, can last well beyond the accounting depreciation of the asset, ultimately saving taxpayer dollars. Given DOE’s recently announced built environment sustainability goals, now is the time to look at interior products as an important part of the overall sustainability plan for LANL’s green building initiatives. The scope of this thesis provides an environmentally sustainable O&M process for the procurement, use, and proper decommissioning of interior products. The thesis also provides environmental and financial data to assist with LANL’s overall DOE Matrix milestones, currently due in 2030.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Polk Carbon Storage Complex CarbonSAFE Phase 3 (Final Scientific/Technical Report)

This report summarizes the workplan, technical progress, and high-level findings for the Polk Carbon Storage Complex (PCSC) CarbonSAFE Phase III project. The project was designed to advance a commercial-scale geologic CO 2 storage by drilling and completing two characterization wells to strengthen an already-submitted Underground Injection Control (UIC) Class VI permit application, acquiring new subsurface data, advancing National Environmental Policy Act (NEPA) requirements, progressing CO 2 transportation engineering, and developing commercial and community engagement frameworks.

54 ENVIRONMENTAL SCIENCES↗

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually updated as new genes are discovered.

59 BASIC BIOLOGICAL SCIENCES↗