SEARCH · Engineering Papers

Results for “building contamination”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8

All sources NASA NTRS DOE OSTI

DOE OSTI2021

Grazer-induced changes in molecular signatures of cyanobacteria

Algal biomass production is an emerging renewable source of fuels, nutrients, manufacturing materials, and pharmaceuticals. Industrial-scale production is predominantly performed in open raceway ponds that are inexpensive to build, operate, and maintain compared to closed bioreactors. However, these open pond systems suffer from increased opportunities for biological contamination from predators, pathogens, and competitors, which result in reduced biomass quality and yields and often the complete destruction of the crop over a short period of time. Early detection of contaminants is a necessary step of integrated pest management for triggering and informing interventions to prevent crop losses. To develop a sensitive method of detection utilizing mass spectrometry (MS), we used three methods – imaging mass spectrometry (imaging MS), liquid chromatography MS/MS (LC-MS/MS) combined with molecular networking, and gas chromatography MS/MS (GC–MS/MS) – to observe and identify molecular signatures from a model predator-prey system of the heterolobosean amoeba HGG1 preying on the filamentous cyanobacterium Anabaena sp. PCC 7120. Imaging MS enabled the association of molecules with the crop, the predator, or the activity of protozoan grazing, while LC-MS/MS-based molecular networking identified a subset of the grazing-specific signals as the chlorophyll breakdown products pyropheophytin, pheophorbide A, and pyropheophorbide. Application of MS techniques to other amoebacyanobacterial predator-prey pairs allowed categorization of grazing signatures as universal or specific to the species of prey, predator, or the prey-predator pairing, indicating that MS-based techniques can distinguish crops from competitors and potentially identify predators. Finally, GCMS/MS was shown to be capable of monitoring novel volatile organic compounds (VOCs), including those predicted to be released through chlorophyll breakdown, in the headspace over algal cultures under predation. Furthermore, these results demonstrate that the combination of multiple MS technologies creates a predictive framework to identify and catalog relevant molecular signatures for informing crop protection strategies.

09 BIOMASS FUELS↗

DOE OSTI2024

Large-scale 2D heterostructures from hydrogen-bonded organic frameworks and graphene with distinct Dirac and flat bands

The current strategies for building 2D organic-inorganic heterojunctions involve mostly wet-chemistry processes or exfoliation and transfer, leading to interface contaminations, poor crystallizing, or limited size. Here we show a bottom-up procedure to fabricate 2D large-scale heterostructure with clean interface and highly-crystalline sheets. As a prototypical example, a well-ordered hydrogen-bonded organic framework is self-assembled on the highly-oriented-pyrolytic-graphite substrate. The organic framework adopts a honeycomb lattice with faulted/unfaulted halves in a unit cell, resemble to molecular “graphene”. Interestingly, the topmost layer of substrate is self-lifted by organic framework via strong interlayer coupling, to form effectively a floating organic framework/graphene heterostructure. The individual layer of heterostructure inherits its intrinsic property, exhibiting distinct Dirac bands of graphene and narrow bands of organic framework. Our results demonstrate a promising approach to fabricate 2D organic-inorganic heterostructure with large-scale uniformity and highly-crystalline via the self-lifting effect, which is generally applicable to most of van der Waals materials.

36 MATERIALS SCIENCE↗

NASA NTRS2022

Clean Air Shower Curtain for Protection of Contamination Sensitive Telescopes on the Ariane 5 Launcher

The launch of the James Webb Space Telescope (JWST) was successfully performed by Ariane 5 from French Guiana on December 25th 2021. The unique nature of the JWST mission led to various adaptations of the Ariane 5 launch system to fulfill stringent cleanliness and hygrometry requirements all along the launch preparation. JWST integration and test activities in the Final Assembly Building (BAF) had to be performed in ISO Class 7 equivalent conditions under Volatile Organic Compounds (VOC) protection and monitoring. For this purpose, a dedicated air supply system equipped with Airborne Molecular Contamination (AMC) filters was installed in the umbilical mast. The fairing itself was specially sealed to protect the inner environment, and to, guarantee ISO Class 7, the BAF Composite Hall (BAF-HC) facilities were upgraded with a removable “Air Shower Curtain” (AShC) containment enclosure between the mobile platforms around JWST. The preparation of these Ariane 5 launch system adaptations started several years before the launch campaign with close cooperation and coordination between Arianespace, ArianeGroup, the European Space Agency (ESA) and the National Aeronautics and Space Administration (NASA). This paper describes their specificities and addresses the challenges experienced to achieve the successful mission preparation.

Contamination Control, James Webb Space Telescope,↗

NASA NTRS2022

Clean Air Shower Curtain for Protection of Contamination Sensitive Telescopes on the Ariane 5 Launcher

Contamination Control, James Webb Space Telescope,↗

DOE OSTI2025

The health and indoor environmental quality impacts of residential building envelope retrofits: A literature review

Retrofitting existing buildings to improve energy efficiency is an important strategy to meet increasingly stringent energy efficiency targets. While the primary objective of energy efficiency retrofits is to reduce energy consumption and greenhouse gas emissions, retrofits can also result in non-energy impacts (NEIs), which contribute to decision-making processes and overall value of the retrofit. NEIs have been studied extensively in retrofitted residential buildings; however, these studies have historically grouped passive (i.e., building envelope) and active (i.e., heating, ventilation, and air conditioning (HVAC) and energy system) upgrades, making it difficult to identify the underlying mechanism(s) of action for each NEI and developing effective retrofit strategies, based on occupant need. The purpose of this study was to better account for NEIs, based on a literature review, summarizing the current state of knowledge on NEIs associated with residential building envelope retrofits. We limited our search to health- and indoor environmental quality-related NEIs. The review identified strong evidence that building envelope retrofits improve acoustic comfort, wintertime thermal comfort, and respiratory and cardiovascular health outcomes. IAQ outcomes were mixed, with studies reporting both increases and decreases to indoor contaminant concentrations following retrofits. The strength of the effect was generally governed by pre-retrofit contaminant concentrations and whether indoor concentrations were dominated by indoor or outdoor sources. Most studies evaluating summertime thermal comfort identified increased incidence of summertime overheating; however, none of these studies linked the change in thermal conditions to health outcomes. Recommendations for future work include expanding studies to include more market rate housing and the health impacts of summertime overheating in retrofitted buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2021

Penetration of Fission Products Ions into Complex Solids and the Effect of Ionic Wash Methods

During washing of radiologically impacted building surfaces, penetration of radionuclide ions into complex solids associated with these surfaces may occur. This study investigates the penetration of Cs-137, Sr-85, and Eu-152 solutions into numerous common building materials and radionuclide behavior when these materials were exposed to a static bath or low-pressure flow of tap water, 0.1 M potassium chloride (KCl), and 0.5 M KCl. The decontamination efficacy and the depth profile for residual contamination were measured to determine the conditions under which applying a wash solution has benefit compared to physically removing the surface material. On asphalt, 70-80% of the radionuclides were found to be within 0.02 mm of the surface. Concrete is more porous than asphalt, and 80% of the radionuclides were within 0.2 mm of the surface for Cs-137 and Eu-152 and 50-80% for Sr-85. Water effectively removed all contaminants from hard nonporous surfaces. Finally, this paper illustrates that a wash penalty factor concept-defined as ratio of the depth at which 50% of the radioactivity is found in the washed sample divided by the depth at which 50% of radioactivity is found in the control-can serve as a way to quantify whether the wash method increases the depth at which contamination penetrates into the material and thus the material becomes more difficult to decontaminate.

building materials↗

NASA NTRS2017

Rust Contamination from Water Leaks in the Cosmic Dust Lab and Lunar and Meteorite Thin Sections Labs at Johnson Space Center

On the early morning of September 15th, 2016, on the first floor of Building 31 at NASA-Johnson Space Center, the hose from a water chiller ruptured and began spraying water onto the floor. The water had been circulating though old metal pipes, and the leaked water contained rust-colored particulates. The water flooded much of the western wing of the building's ground floor before the leak was stopped, and it left behind a residue of rust across the floor, most notably in the Apollo and Meteorite Thin Section Labs and Sample Preparation Lab. No samples were damaged in the event, and the affected facilities are in the process of remediation. At the beginning of 2016, a separate leak occurred in the Cosmic Dust Lab, located in the same building. In that lab, a water leak occurred at the bottom of the sink used to clean the lab's tools and containers with ultra-pure water. Over years of use, the ultra-pure water eroded the metal sink piping and leaked water onto the inside of the lab's flow bench. This water also left behind a film of rusty material. The material was cleaned up and the metal piping was replaced with PVC pipe and sealed with Teflon plumber's tape. Samples of the rust detritus were collected from both incidents. These samples were imaged and analyzed to determine their chemical and mineralogical compositions. The purpose of these analyses is to document the nature of the detritus for future reference in the unlikely event that these materials occur as contaminants in the Cosmic Dust samples or Apollo or Meteorite thin sections.

Kent, J. J.↗

NASA NTRS2002

An IDEA of What's in the Air

The Automatic Particle Fallout Monitor (APFM) is an automated instrument that assesses real-time particle contamination levels in a facility by directly imaging, sizing, and counting contamination particles. It allows personnel to respond to particle contamination before it becomes a major problem. For NASA, the APFM improves the ability to mitigate, avoid, and explain mission-compromising incidents of contamination occurring during payload processing, launch vehicle ground processing, and potentially, during flight operations. Commercial applications are in semiconductor processing and electronics fabrication, as well as aerospace, aeronautical, and medical industries. The product could also be used to measure the air quality of hotels, apartment complexes, and corporate buildings. IDEA sold and delivered its first four units to the United Space Alliance for the Space Shuttle Program at Kennedy. NASA used the APFM in the Kennedy Space Station Processing Facility to monitor contamination levels during the assembly of International Space Station components.

Source record↗

DOE OSTI2023

Using Multiple Geophysical Methods to Refine a Stratigraphic Conceptual Site Model at a Nuclear Waste Site

At contaminated sites, there is a critical reliance on conceptual site models of which a key component is the geologic framework model (GFM), which is used to build predictive fate and transport modeling in support of remediation goals. Here, we detail an ongoing study at a nuclear waste site (Hanford Site, Washington, USA) where surface geophysical methods were used to complement existing borehole information and to help site new boreholes to update and refine the GFM. Ground-based electrical resistivity tomography (ERT), time-domain electromagnetics (TEM), and seismic data was acquired on the Hanford Site’s Central Plateau, where the presence of a hydraulically transmissive subsurface feature, or paleochannel, was suspected but uncertain based on contaminant concentrations at sparsely located boreholes. To assess and compare ERT, TEM, and seismic geophysical datasets, co-located data was acquired in an area where the existing GFM was more certain. Surrounding the suspected paleochannel, ERT and seismic refraction tomography showed similar subsurface structures consistent with a channelized feature. While TEM interpretation was limited in the suspected paleochannel area due to a thick resistive top layer and high electromagnetic noise, TEM showed greater utility in a different area where these factors were less prevalent. Based on the results of quasi-3D ERT inversions, we propose updates to the GFM, including identifying a paleochannel. Further, we evaluate the utility of geophysical methods and examine lessons learned that will be used as a basis for continued characterization efforts to support site management decisions and implementation efforts.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

NASA NTRS2005

NSTAR Extended Life Test Discharge Chamber Flake Analysis

The Extended Life Test (ELT) of the NASA Solar Electric Propulsion Technology Readiness (NSTAR) ion thruster was concluded after 30,352 hours of operation. The ELT was conducted using the Deep Space 1 (DS1) back-up flight engine, a 30 cm diameter xenon ion thruster. Post-test inspection of the ELT engine revealed numerous contaminant flakes distributed over the bottom of the cylindrical section of the anode within the discharge chamber (DC). Extensive analyses were conducted to determine the source of the particles, which is critical to the understanding of degradation mechanisms of long life ion thruster operation. Analyses included: optical microscopy (OM) and particle length histograms, field emission scanning electron microscopy (FESEM) combined with energy dispersive spectroscopy (EDS), and atomic oxygen plasma exposure tests. Analyses of the particles indicate that the majority of the DC flakes consist of a layered structure, typically with either two or three layers. The flakes comprising two layers were typically found to have a molybdenum-rich (Mo-rich) layer on one side and a carbon-rich (C-rich) layer on the other side. The flakes comprising three layers were found to be sandwich-like structures with Mo-rich exterior layers and a C-rich interior layer. The presence of the C-rich layers indicates that these particles were produced by sputter deposition build-up on a surface external to the discharge chamber from ion sputter erosion of the graphite target in the test chamber. This contaminant layer became thick enough that particles spalled off, and then were electro-statically attracted into the ion thruster interior, where they were coated with Mo from internal sputter erosion of the screen grid and cathode components. Atomic oxygen tests provided evidence that the DC chamber flakes are composed of a significant fraction of carbon. Particle size histograms further indicated that the source of the particles was spalling of carbon flakes from downstream surfaces. Analyses of flakes taken from the downstream surface of the accelerator grid provided additional supportive information. The production of the downstream carbon flakes, and hence the potential problems associated with the flake particles in the ELT ion thruster engine is a facility induced effect and would not occur in the space environment.

deGroh, Kim K.↗

DOE OSTI2020

Feedback on Forty-year Long Clean-up Operations of a Contaminated Soil for Environmental Purpose - 20026

One of the CEA facilities in France is the place of miscellaneous mapping and clean-up operations since the 1980's. The final purpose of the conducted work deals with the environmental remediation of the building. In France, the absence of a regulatory framework for the management of sites polluted by radioactive substances, especially as the lack of release thresholds, has led to develop different approaches of soil radiological characterization. The geostatistical approach is part of them. Preliminary investigations are an unavoidable step prior to clearance and remediation. First, historical analysis enables to define site perimeters to investigate as well as to precisely locate expected contaminated parts. For radioactive pollutants, the media (water, soil, air) and transfer routes participate in the definition of the investigation perimeter and thus also need to be identified through a geological study. At the same time, functional analysis leads to choose the best measurement means which could provide useful information when combined with visual inspection. An equipment well adapted to easy-to-measure radionuclides as gamma emitters, such as gamma probe or on-site gamma spectrometry, is usually selected as a non-destructive assay. Coupled with spatial positions, processed on-site radiological data can be mapped. Data processing consists in mapping and kriging before a geostatistical analysis in order to identify the zones of interest to be targeted. Selected zones are not only linked to high level count rates but also to low level ones so that a pollution-free reference is known in the area. This data processing also enables to categorize waste types according to their origin and contamination levels. An expected volume of different waste then follows as well as the waste characterization equipments. In-depth investigations, e.g. core drillings and samplings, naturally ensue to aim at remediation optimization through the assessment of environmental impact. After clean-up operations, non-destructive assays as well as destructive samplings enable to check the effective clearance. Following this methodology in the present remediation work, results of the first non-destructive assay campaign highlighted a long-lived transuranic radionuclides contamination in the concrete flagstone. Successive non-destructive assays were then performed in the defined zones of interest. Count rates measured with a surface probe were first mapped. The best localization of destructive assays, i.e. core drillings at a 1 meter depth, came from this surface mapping followed by a geostatistical analysis. The concrete flagstone was totally removed. Then, the depth of soil to remove under the flagstone was optimized from the results of radiological activities measured in core drillings samples. A new surface mapping was then drawn after this partial soil excavation. The sand and demolition rubble samples, homogeneously constituted from the flagstone fragments, were analyzed by gamma spectrometry. Meanwhile, waste drums and other containers were also measured by gamma spectrometry and passive neutron measurement devices. All these results have brought miscellaneous pieces of information. In this context, major issues appear in terms of physical constraints such as the premises tininess as well as of soil sampling techniques and in terms of measurement performances assessment and the representativeness of homogeneous samples. The choice of radiological soil and waste characterization devices is described in the light of enhanced performances by keeping in mind radiation protection requirements and a willing to always optimize waste categories (very low level waste) and volume. The improvement of the characterization methods appears through this forty-year long work while sharing the feedback of encountered difficulties. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

NASA NTRS2012

Concept for Hydrogen-Impregnated Nanofiber/Photovoltaic Cargo Stowage System

A stowage system was conceived that consists of collapsible, reconfigurable stowage bags, rigid polyethylene or metal inserts, stainless-steel hooks, flexible photovoltaic materials, and webbing curtains that provide power generation, thermal stabilization, impact resistance, work/sleeping surfaces, and radiation protection to spaceflight hardware and crew members. Providing materials to the Lunar surface is costly from both a mass and a volume standpoint. Most of the materials that will be transferred to other planets or celestial bodies will not be returned to the Earth. In developing a plan to reconfigure pressurized logistics modules, it was determined that there was a requirement to be able to utilize the interior volume of these modules and transform them from Logistics Modules to Storage/Living Quarters. Logistics-to-living must re-utilize stowage bags and the structures that support them to construct living spaces, partitions, furniture, protective shelters from solar particle events, galactic cosmic radiation, and workspaces. In addition to reusing these logistics items for development of the interior living spaces, these items could also be reused outside the habitable volumes to build berms that protect assets from secondary blast ejecta, to define pathways, to stabilize high traffic areas, to protect against dust contamination, to secure assets to mobility elements, to provide thermal protection, and to create other types of protective shelters for surface experiments. Unique features of this innovation include hydrogen-impregnated nano fibers encapsulated in a polyethelyne coating that act as radiation shielding, flexible solar collection cells that can be connected together with cells from other bags via the webbing walls to create a solar array, and the ability to reconfigure each bag to satisfy multiple needs.

Kennedy, Kriss J.↗

DOE OSTI2022

Healthy Buildings Guide for Small Businesses: A Quick Reference to Improve Indoor Air Quality (Restaurants Excluded)

Indoor air pollutant concentrations can be higher than those outdoors, putting occupants at risk. These pollutants come from a variety of sources: materials used to build and furnish indoor spaces, retail products and services, and occupants themselves. Ventilation, temperature, and humidity also affect indoor air quality. It is important to consider the documented benefits of healthy indoor environments at any time – not just during a public health crisis – and it is key to consider the indoor air quality where we do business as well as at home. Small businesses vary in size, services, products, ownership style, and building mechanical systems, yet all benefit from healthy indoor spaces for employees and customers. This guide provides steps, in conjunction with public health guidance, that small businesses can take to improve and maintain indoor air quality. Small businesses often have unique ownership structures – the building owner and business owner can be different parties – so this guide addresses both building and business owner action items. There are many ways to pursue healthy indoor air, including eliminating, minimizing, and/or controlling the contaminants we bring in, and removing or diluting any existing contaminants through ventilation, filtration, air cleaning, and/or disinfection. Best results are achieved through a comprehensive approach combining various strategies, including those discussed in this guide.

air filtration↗

DOE OSTI2022

Guia de Edificios Saludables para Pequenas Empresas: Una Referencia Rapida para Mejorar la Calidad del Aire Interior (Restaurantes Excluidos)

Indoor air pollutant concentrations can be higher than those outdoors, putting occupants at risk. These pollutants come from a variety of sources: materials used to build and furnish indoor spaces, retail products and services, and occupants themselves. Ventilation, temperature, and humidity also affect indoor air quality. It is important to consider the documented benefits of healthy indoor environments at any time - not just during a public health crisis - and it is key to consider the indoor air quality where we do business as well as at home. Small businesses vary in size, services, products, ownership style, and building mechanical systems, yet all benefit from healthy indoor spaces for employees and customers. This guide provides steps, in conjunction with public health guidance, that small businesses can take to improve and maintain indoor air quality. Small businesses often have unique ownership structures - the building owner and business owner can be different parties - so this guide addresses both building and business owner action items. There are many ways to pursue healthy indoor air, including eliminating, minimizing, and/or controlling the contaminants we bring in, and removing or diluting any existing contaminants through ventilation, filtration, air cleaning, and/or disinfection. Best results are achieved through a comprehensive approach combining various strategies, including those discussed in this guide.

air filtration↗

DOE OSTI2026

WM26 Paper Multi-Robot Collaboration for Hazardous Environments

Hazardous nuclear and industrial facilities are rarely designed for robots. Work in these domains demand precise manipulation and robust mobility in cluttered, constrained spaces where off-the-shelf platforms struggle and “one-size-fits-all” machines become costly and complex. Idaho National Laboratory (INL) is developing an autonomous, multi-robot inspection system that coordinates task-specific platforms rather than relying on a single omni-tool robot. An electric truck serves as a power and compute hub for a custom manipulator co-developed with Florida International University (FIU), a commercial mini crawler, a pan–tilt–zoom camera, and a Nexxis Argus LiDAR mapping system. Working in concert, these robots generate spatial, radiation, and temperature maps of the pit environments at the Hanford Waste Tank Farms. These systems will capture visual records and environmental telemetry to allow for analysis post inspection. The system architecture uses Robot Operating System 2 (ROS 2) for publish/subscribe integration, NVIDIA Isaac Sim and Unity for simulation and visualization, and algorithms such as NVBlox to fuse data into unified 3D overlays. This robot-agnostic approach reduces operator burden by enabling autonomy across heterogeneous platforms and lets each robot be used where it is strongest. Having autonomous functions means operators don’t have to fully control multiple different components. The ease of use could allow for more widespread adoption of advanced robotics at waste management sites that see continued use. By coordinating simpler, purpose-built mechanisms, the approach lowers design and manufacturing complexity, reduces capital risk in contaminated settings, and improves controllability for complex inspection and manipulation tasks. We present the architecture, early results, and lessons learned from building and deploying this coordinated multi-robot system, with the goal of accelerating safe, cost-effective adoption of advanced robotics at waste-management sites.

42 - ENGINEERING↗

NASA NTRS2013

Spectroscopic Determination of Trace Contaminants in High-Purity Oxygen

Oxygen used for extravehicular activities (EVAs) must be free of contaminants because a difference in a few tenths of a percent of argon or nitrogen content can mean significant reduction in available EVA time. These inert gases build up in the extravehicular mobility unit because they are not metabolized or scrubbed from the atmosphere. A prototype optical emission technique capable of detecting argon and nitrogen below 0.1% in oxygen has been developed. This instrument uses a glow discharge in reduced-pressure gas to produce atomic emission from the species present. Because the atomic emission lines from oxygen, nitrogen, and argon are discrete, and in many cases well-separated, trace amounts of argon and nitrogen can be detected in the ultraviolet and visible spectrum. This is a straightforward, direct measurement of the target contaminants, and may lend itself to a device capable of on-orbit verification of oxygen purity. A glow discharge is a plasma formed in a low-pressure (1 to 10 Torr) gas cell between two electrodes. Depending on the configuration, voltages ranging from 200 V and above are required to sustain the discharge. In the discharge region, the gas is ionized and a certain population is in the excited state. Light is produced by the transitions from the excited states formed in the plasma to the ground state. The spectrum consists of discrete, narrow emission lines for the atomic species, and broader peaks that may appear as a manifold for molecular species such as O2 and N2, the wavelengths and intensities of which are a characteristic of each atom. The oxygen emission is dominated by two peaks at 777 and 844 nm.

Hornung, Steven↗

DOE OSTI2020

A method for achieving complete microbial genomes and improving bins from metagenomics data

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes ( i.e ., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Less than 100 circularized bacterial and archaeal genomes have been assembled from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a method to achieve circularized genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. We present 34 circular CPR genomes, one circular Margulisbacteria genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg .

Lui, Lauren↗

DOE OSTI2021

A method for achieving complete microbial genomes and improving bins from metagenomics data

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.

59 BASIC BIOLOGICAL SCIENCES↗