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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Whole-genome sequencing and single nucleotide polymorphisms in multidrug-resistant clinical isolates of Mycobacterium tuberculosis from the Philippines

Thousands of cases of multidrug-resistant tuberculosis (TB) have been observed in the Philippines, but studies on the Mycobacterium tuberculosis (MTB) genotypes that underlie the observed drug resistance profiles are lacking. This study aimed to analyse the whole genomes of clinical MTB isolates representing various resistance profiles to identify single nucleotide polymorphisms (SNPs) in resistance-associated genes. The genomes of ten MTB isolates cultured from banked sputum sources were sequenced. Bioinformatics analysis consisted of assembly, annotation and SNP identification in genes reported to be associated with resistance to isoniazid (INH), rifampicin (RIF), ethambutol (ETH), streptomycin, pyrazinamide (PZA) and fluoroquinolones (FQs). The draft assemblies covered an average of 97.08% of the expected genome size. Seven of the ten isolates belonged to the Indo-Oceanic lineage/EA12-Manila clade. Two isolates were classified into the Euro-American lineage, whilst the pre-XDR (pre-extensively drug-resistant) isolate was classified under the East Asian/Beijing clade. The SNPs katG Ser315Thr, rpoB Ser450Leu and embB Met306Val were found in INH- (4/7), RIF- (3/6) and ETH-resistant (2/6) isolates, respectively, but not in susceptible isolates. Mutations in the inhA promoter and in the pncA and gyrA genes known to be involved in resistance to INH, PZA and FQs, respectively, were also identified. This study represents the first effort to investigate the whole genomes of Philippine clinical strains of MTB exhibiting various multidrug resistance profiles. Whole-genome data can provide valuable insights to the mechanistic and epidemiological qualities of TB in a high-burden setting such as the Philippines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Mechanical failure of fresh nuclear grade iron–chromium–aluminum (FeCrAl) cladding under simulated hot zero power reactivity initiated accident conditions

The reactivity initiated accident (RIA) is a postulated accident in light water reactors initiated by a rapid increase in reactivity which causes an increase in fission rate and fuel temperature. One potential mode of fuel system failure during RIA is pellet cladding mechanical interaction (PCMI) due to the rapid thermal expansion of the fuel pellet. Simulated PCMI experiments were performed by rapidly pressurizing iron-chromium-aluminum (FeCrAl) cladding tube samples using a hydraulic modified burst test system, causing the specimens to burst under a biaxial loading path. Deformation and rupture of the specimens were tracked with a telecentric lens and high-speed camera system. Outer surface strains were calculated using digital image correlation (DIC) on speckle patterns painted on the specimens’ outer surfaces. Experiments were conducted at approximately 275 °C, representative of hot zero power RIA conditions. The failure hoop strain was DIC-calculated between approximately 1.8–3.4%, corresponding to quasi-static energy depositions of approximately 110–260 calories per gram UO 2 assuming initial pellet-cladding contact. These conditions are very similar to the proposed energy deposition limit of 150 calories per gram UO 2 for unirradiated zirconium-based cladding in US Nuclear Regulatory Commission (NRC) Draft Regulatory Guide 1327. A very small strain rate dependence was observed in the data, with the magnitude of the failure hoop strain decreasing slightly with increasing strain rate. This observed dependence may be relevant because the FeCrAl cladding strain rate will be approximately 20% higher than in zirconium-based cladding due to the harder neutron spectrum and resultant shorter neutron generation time.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Device for steam cladding oxidation testing at TREAT

To compare the chemical degradation of conventional zirconium alloy (Zry) cladding to advance silicon carbide (SiC) cladding in a post loss of coolant accident (LOCA) environment, new nuclear testing capabilities are necessary. The Transient Reactor Test (TREAT) Facility at Idaho National Laboratory (INL) has matured its transient fuel testing capabilities since its 2017 restart. The most recent experiment architecture is the Transient Water Irradiation System in TREAT (TWIST), which is designed to support qualification of accident tolerant fuels in light water reactors. INL has designed and analyzed a natural circulation steam flow modification for TWIST to produce prototypic conditions of cladding oxidation. The in-situ device will be electrically heated to drive natural circulation. Moreover, the SiC cladding requires heating above 1700 °C to observe failure, thus internal prototypic nuclear heating with radiation effects will be used. Thermal hydraulic analysis with RELAP5-3D (Reactor Excursion and Leak Analysis Program) estimated steam fluxes greater than 50 mg cm −2 s −1 can be achieved. These fluxes are adequate to test Zry cladding according to draft regulatory guides and to test SiC cladding according to past experiments.

Oxidation↗
DOE OSTI2020

A coupled polygonal DEM-LBM technique based on an immersed boundary method and energy-conserving contact algorithm

Here we present a framework of coupling polygonal discrete elements and the lattice Boltzmann method using a direct forcing immersed boundary scheme. In this technique, an energy-conserving contact algorithm is utilized to handle the interactions between convex and concave polygonal particles. The surface of a polygon is represented by discrete boundary points which includes vertices of polygonal particles and/or points interpolated from vertices. The fluid-particle coupling is obtained through the interactions of the boundary points and the imaginary fluid particles using a direct-forcing immersed boundary method. Validations of the proposed technique are made by single particle and multiple arbitrarily-shaped particle sedimentation tests, and the effect of particle shape is illustrated using a drafting-kissing-tumbling benchmark.

42 ENGINEERING↗
DOE OSTI2018

Evaluation of the performance of distributed and centralized biomass technologies in rural China

Biomass fermentation and gasification are two types of biomass utilization technologies for residential households. Government plays an essential role in the diffusion of improved technologies. Cost-effectiveness analysis can provide the cost and abatement potentials of each alternative under a single abatement strategy; however, it is difficult for policy-makers to make an integrated assessment when multiple objectives are involved. This paper evaluates the performance of three distributed alternatives and two centralized alternatives for residential biomass use in rural China, including centralized biogas and centralized gasifier systems. An integrated assessment approach is built, which combines cost-benefit analysis, an entropy-weighting method, and a preference-ranking organization method for enrichment evaluations using the PROMETHEE approach. A total of 686 sample households in three regions of China were surveyed in this study. The centralized gasifier system and distributed household biogas were the top two alternatives for further development to meet the government’s 2020 development goal for biogas technology. The overall biomass utilization amount in the prioritized scenario is about three times that of the business-as-usual scenario by 2020. Furthermore, this study can provide significant insights for China’s policy-makers to draft strategic policies and countermeasures that will promote the development of renewable energy in China.

09 BIOMASS FUELS↗
DOE OSTI2017

A status review of photovoltaic power conversion equipment reliability, safety, and quality assurance protocols

Data indicate that the inverter is the element of the photovoltaic plant that has the highest number of service calls and the greatest operation and maintenance cost burden. This paper describes the projects and relevant background needed in developing design qualification standards that would serve to establish a minimum level of reliability, along with a review of photovoltaic inverter quality and safety standards, most of which are in their infancy. We compare stresses and levels for accelerated testing of inverters proposed in the standard drafts, and those proposed by manufacturers and purchasers of inverters. We also review bases for the methods, stress types, and stress levels for durability testing of key inverter components. Many of the test protocols appear to need more comprehensive inclusion of stress factors existing in the natural environment such as wind driven rain, dust, and grid disturbances. Further understanding of how temperature, humidity ingress, and voltage bias affect the inverters and their components is also required. We provide data indicating inconsistent quality of the inverters and the durability of components leading to greater cost for the photovoltaic plant operator. Accordingly, the recommendation for data collection within quality standards for obtaining cost of ownership metrics is made. Design validation testing using realistic operation, environmental, and connection conditions, including under end-use field conditions with feedback for continuous improvement is recommended for inclusion within a quality standard.

14 SOLAR ENERGY↗
DOE OSTI2013

A novel QSAR model of Salmonella mutagenicity and its application in the safety assessment of drug impurities

As indicated in ICH M7 draft guidance, in silico predictive tools including statistically-based QSARs and expert analysis may be used as a computational assessment for bacterial mutagenicity for the qualification of impurities in pharmaceuticals. To address this need, we developed and validated a QSAR model to predict Salmonella t. mutagenicity (Ames assay outcome) of pharmaceutical impurities using Prous Institute's Symmetry℠, a new in silico solution for drug discovery and toxicity screening, and the Mold2 molecular descriptor package (FDA/NCTR). Data was sourced from public benchmark databases with known Ames assay mutagenicity outcomes for 7300 chemicals (57% mutagens). Of these data, 90% was used to train the model and the remaining 10% was set aside as a holdout set for validation. The model's applicability to drug impurities was tested using a FDA/CDER database of 951 structures, of which 94% were found within the model's applicability domain. The predictive performance of the model is acceptable for supporting regulatory decision-making with 84 ± 1% sensitivity, 81 ± 1% specificity, 83 ± 1% concordance and 79 ± 1% negative predictivity based on internal cross-validation, while the holdout dataset yielded 83% sensitivity, 77% specificity, 80% concordance and 78% negative predictivity. Given the importance of having confidence in negative predictions, an additional external validation of the model was also carried out, using marketed drugs known to be Ames-negative, and obtained 98% coverage and 81% specificity. Additionally, Ames mutagenicity data from FDA/CFSAN was used to create another data set of 1535 chemicals for external validation of the model, yielding 98% coverage, 73% sensitivity, 86% specificity, 81% concordance and 84% negative predictivity. - Highlights: • A new in silico QSAR model to predict Ames mutagenicity is described. • The model is extensively validated with chemicals from the FDA and the public domain. • Validation tests show desirable high sensitivity and high negative predictivity. • The model predicted 14 reportedly difficult to predict drug impurities with accuracy. • The model is suitable to support risk evaluation of potentially mutagenic compounds.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Improvement actions in waste management systems at the provincial scale based on a life cycle assessment evaluation

Highlights: • LCA was used for evaluating the performance of four provincial waste management systems. • Milano, Bergamo, Pavia and Mantova (Italy) are the provinces selected for the analysis. • Most of the data used to model the systems are primary. • Significant differences were found among the provinces located in the same Region. • LCA was used as a decision-supporting tool by Regione Lombardia. - Abstract: This paper reports some of the findings of the ‘GERLA’ project: GEstione Rifiuti in Lombardia – Analisi del ciclo di vita (Waste management in Lombardia – Life cycle assessment). The project was devoted to support Lombardia Region in the drafting of the new waste management plan by applying a life cycle thinking perspective. The present paper mainly focuses on four Provinces in the Region, which were selected based on their peculiarities. Life cycle assessment (LCA) was adopted as the methodology to assess the current performance of the integrated waste management systems, to discuss strengths and weaknesses of each of them and to design their perspective evolution as of year 2020. Results show that despite a usual business approach that is beneficial to all the provinces, the introduction of technological and management improvements to the system provides in general additional energy and environmental benefits for all four provinces. The same improvements can be easily extended to the whole Region, leading to increased environmental benefits from the waste management sector, in line with the targets set by the European Union for 2020.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2015

Multi-criteria evaluation in strategic environmental assessment for waste management plan, a case study: The city of Belgrade

Highlights: • The paper deals with the specific method of multi-criteria evaluation applied in drafting the SEA for the Belgrade WMP. • MCE of the planning solutions, assessed according to 37 objectives of the SEA and four sets of criteria, was presented in the matrix form. • The results are presented in the form of graphs so as to be easily comprehensible to all the participants in the decision-making process. • The results represent concrete contribution proven in practice. - Abstract: Strategic Environmental Assessment (SEA) is one of the key instruments for implementing sustainable development strategies in planning in general; in addition to being used in sectoral planning, it can also be used in other areas such as waste management planning. SEA in waste management planning has become a tool for considering the benefits and consequences of the proposed changes in space, also taking into account the capacity of space to sustain the implementation of the planned activities. In order to envisage both the positive and negative implications of a waste management plan for the elements of sustainable development, an adequate methodological approach to evaluating the potential impacts must be adopted and the evaluation results presented in a simple and clear way, so as to allow planners to make relevant decisions as a precondition for the sustainability of the activities planned in the waste management sector. This paper examines the multi-criteria evaluation method for carrying out an SEA for the Waste Management Plan for the city of Belgrade (BWMP). The method was applied to the evaluation of the impacts of the activities planned in the waste management sector on the basis of the environmental and socioeconomic indicators of sustainability, taking into consideration the intensity, spatial extent, probability and frequency of impact, by means of a specific planning approach and simple and clear presentation of the obtained results.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Solid waste generation and characterization in the University of Lagos for a sustainable waste management

Waste characterization is the first step to any successful waste management policy. In this paper, the characterization and the trend of solid waste generated in University of Lagos, Nigeria was carried out using ASTM (D5231-92) and Resource Conservation Reservation Authority RCRA Waste Sampling Draft Technical Guidance methods. The recyclable potential of the waste is very high constituting about 75% of the total waste generated. The estimated average daily solid waste generation in Unilag Akoka campus was estimated to be 32.2 tons. The solid waste characterization was found to be: polythene bags 24% (7.73 tons/day), paper 15% (4.83 tons/day), organic matters 15%, (4.83 tons/day), plastic 9% (2.90 tons/day), inert materials 8% (2.58 tons/day), sanitary 7% (2.25 tons/day), textile 7% (2.25 tons/day), others 6% (1.93 tons/day), leather 4% (1.29 tons/day) metals 3% (0.97 tons/day), glass 2% (0.64 tons/day) and e-waste 0% (0.0 tons/day). The volume and distribution of polythene bags generated on campus had a positive significant statistical correlation with the distribution of commercial and academic structures on campus. Waste management options to optimize reuse, recycling and reduce waste generation were discussed.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

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

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

Dirks, Alden C↗
DOE OSTI2023

Grid Spacing Sensitivities of Simulated Mid-Latitude and Tropical Mesoscale Convective Systems in the Convective Gray Zone

The main objective of this study is to observationally constrain processes in tropical and midlatitude mesoscale convective systems (MCSs), and to use these constraints for model evaluation. To accomplish this, we leverage MCS observations collected at the U.S. DOE Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) site in Oklahoma and ARM's mobile GoAmazon2014/15 site in Manaus, Brazil (MAO). We simulate 13 and 11 of these observed MCSs at the SGP and MAO site, respectively, using the Weather Research and Forecasting model at 12-, 4-, 2-, and 1-km horizontal grid spacing. Observations from radiosondes, surface meteorology, and radar wind profilers are used to characterize MCS properties, such as MCS timing and location, cold pools, and convective drafts, and evaluate these simulations. SGP cases are found in better agreement with observations than MAO cases, and when simulated at 2 km, outperform simulations at 1 km regarding the timing of MCS overpass and the accuracy of surface variable trends. MAO simulations suggest a consistent improvement in model accuracy with increasing model resolution in depicting the downdraft structure, the timing of MCSs, and the surface variables changes, except for the latter two metrics at 2 km. Deficiencies are still evident at km-scales, suggesting the need for higher resolution to simulate tropical MCSs. Overall, location-dependent improvements in MCS representation are obtained with the increasing model resolution, prompting the evaluation of sub-km scale simulations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Resolving Mesoscale Convective Systems: Grid Spacing Sensitivity in the Tropics and Midlatitudes

Abstract Mesoscale convective systems (MCSs) are a critical global water cycle component and drive extreme precipitation events in tropical and midlatitude regions. However, simulating deep convection remains challenging for modern numerical weather and climate models due to the complex interactions of processes from microscales to synoptic scales. Recent models with kilometer‐scale horizontal grid spacings offer notable improvements in simulating deep convection compared to coarser‐resolution models. Still, deficiencies in representing key physical processes, such as entrainment, lead to systematic biases. Additionally, evaluating model outputs using process‐oriented observational data remain difficult. This study presents an ensemble of MCS simulations with spanning the deep convective gray zone ( from 12 km to 125 m) in the Southern Great Plains of the U.S. and the Amazon Basin. Comparing these simulations with Atmospheric Radiation Measurement (ARM) wind profiler observations, we find greater sensitivity in the Amazon Basin compared to the Great Plains. Convective drafts converge structurally at sub‐kilometer scales, but some deficiencies remain. In both regions, simulated up and downdrafts are too deep and extreme downdrafts are not strong enough. Furthermore, Amazonian updrafts are too strong. Overall, we observe higher sensitivity in the tropics, including an artificial buildup in vertical kinetic energy at scales of , suggesting a need for 250 m in this region. Nevertheless, bulk convergence—agreement of storm‐average statistics—is achievable with kilometer‐scale simulations within a 10% error margin with 1 km providing a good balance between accuracy and computational cost.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

The Impacts of Rotational Mixing on the Precipitation Simulated by a Convection Permitting Model

With increased availability of computational resources, regional and global scale convection-permitting model (CPM, Δx ~ 1–10 km) simulations are becoming more common. CPMs have improved accuracy in their representation of deep convection and mesoscale convective systems (MCSs) compared to coarser resolution models. However, CPMs still exhibit convective cloud and precipitation biases relative to observations, notably a lesser frequency of light precipitation rates and greater frequency of heavy precipitation rates. In this work we hypothesize that these CPM biases are related to under-resolved mixing between convective updrafts and their surrounding environment. To test this hypothesis, we introduce a parameterization to the Weather Research and Forecasting model (WRF) that adds a small angular rotation of the grid-scale flow about the axis perpendicular to the plane of convective drafts. This rotated flow is then allowed to alter advection of moisture and hydrometeors. The effects of such mixing on precipitation characteristics are evaluated in month-long 4-km grid spacing simulations over the Amazon. The enhanced mixing transports moisture and condensate from convective cores to other areas including downdrafts. This increases the frequency of low-precipitable water and light precipitation. It also decreases the frequency of intense precipitation from isolated deep convection and MCSs, increases cloud top temperatures, reduces radar echo-top heights, and increases overall precipitation by altering the relationship of precipitation with precipitable water, in better agreement with observations. The results suggest when optimized using multiple observations, such an approach may provide a path toward more accurate representation of convection and precipitation statistics in convection-permitting simulations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

An Optimized Parameterization of Sub‐Grid Scale Advection for Convection Permitting Models

Convection‐permitting models (CPMs) explicitly resolve deep convection yet under‐resolve the organized lateral exchanges among drafts and their environment that control entrainment/detrainment, precipitation efficiency, and mesoscale structure. In this work, we introduce the Optimized Advection Scheme (OAS), which introduces a small rotation of the Cartesian frame of reference for the horizontal winds relative to other variables used in advection that induces cross‐gradient transport to mimic under‐resolved convective mixing. The rotation angle is selected to minimize the Kullback–Leibler divergence between the simulated and satellite observed precipitation intensity distributions, yielding a physically consistent perturbation that is computationally inexpensive and portable. Optimized Advection Scheme is implemented in WRF and evaluated over Amazon (April 2014). It shifts precipitation–precipitable‐water joint distributions toward lighter rain, reduces overly intense rates, and improves mesoscale convective system (MCS) lifetime and propagation. Mechanistically, the added cross‐gradient transport promotes convective detrainment and environmental mixing, which cools and moistens the mid‐troposphere, weakens downward momentum transport, alleviates excessive downwelling shortwave biases, and warms the surface temperature. The optimized rotation angle yields comparable improvements at 4‐km and 1‐km grid spacing, demonstrating resolution‐independent benefits across the CPM gray zone. By targeting the dynamical root of under‐mixed convective circulations, rather than tuning model microphysics or closures, OAS delivers robust, scale‐aware improvements in precipitation statistics, cloud vertical structure, and characteristics of MCS (MCSs), offering a practical pathway to more reliable CPM simulations for weather and climate applications.

CPM↗
DOE OSTI2013

Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data

Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of 44 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (B450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that 420% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the ‘upper’ HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

Here we report that high-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a ‘divide and conquer’ strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Finally, our study demonstrates the potential of the ‘divide and conquer’ strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

ProDeGe: A computational protocol for fully automated decontamination of genomes

Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plagued by contamination. Since these genomes are now being generated in a high-throughput manner and sequences from them are propagating into public databases to drive novel scientific discoveries, rigorous quality controls and decontamination protocols are urgently needed. Here, we present ProDeGe (Protocol for fully automated Decontamination of Genomes), the first computational protocol for fully automated decontamination of draft genomes. ProDeGe classifies sequences into two classes—clean and contaminant—using a combination of homology and feature-based methodologies. On average, 84% of sequence from the non-target organism is removed from the data set (specificity) and 84% of the sequence from the target organism is retained (sensitivity). Lastly, the procedure operates successfully at a rate of ~0.30 CPU core hours per megabase of sequence and can be applied to any type of genome sequence.

59 BASIC BIOLOGICAL SCIENCES↗