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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 361 records · Page 20

DeFault: DEep‐Learning‐Based FAULT Delineation Using the IBDP Passive Seismic Data at the Decatur CO2 Storage Site

Abstract The carbon capture, utilization, and storage (CCUS) framework is an essential component in reducing greenhouse gas emissions, with its success hinging on the comprehensive knowledge of subsurface geology and geomechanics. Passive seismic event relocation and fault detection offer vital insights into subsurface structures and the ability to monitor fluid migration pathways. Accurate identification and localization of seismic events, however, face significant challenges, including the necessity for high‐quality seismic data and advanced computational methods. To address these challenges, we introduce a novel deep learning method, , specifically designed for passive seismic source relocation and fault delineating for passive seismic monitoring projects. By leveraging data domain‐adaptation, allows us to train a neural network with labeled synthetic data and apply it directly to field data. Using , the passive seismic sources are automatically clustered based on their recording time and spatial locations, and subsequently, faults and fractures are delineated accordingly. We demonstrate the efficacy of on a field case study involving injection related microseismic data from Decatur, Illinois area. Our approach accurately and efficiently relocated passive seismic events, identified faults and could aid in potential damage induced by seismicity. Our results highlight the potential of as a valuable tool for passive seismic monitoring, emphasizing its role in ensuring CCUS project safety. This research bolsters the understanding of subsurface characterization in CCUS, illustrating machine learning’s capacity to refine these methods. Ultimately, our work has significant implications for CCUS technology deployment, an essential strategy in combating climate change. Plain Language Summary In our quest to tackle climate change, we use a strategy known as carbon capture, utilization, and storage (CCUS) to keep greenhouse gases out of the atmosphere. This strategy relies heavily on our ability to understand what's happening deep under the earth's surface. To make sure we store super critical safely, we need to accurately map out the geological structure, especially faults, but this is tough without high‐quality data and complex computer programs. We've developed a new tool called “DeFault,” which uses advanced machine learning to improve how we find and map these underground features. “DeFault” is smart enough to learn from numerically simulated data and then apply what it’s learned to real‐world situations. It groups together seismic activity—tiny tremors and shifts in the earth—based on when and where they happen, which helps us spot where there might be cracks or faults. We tested “DeFault” in Illinois, where CO 2 is injected underground, and it successfully pinpointed where these tremors occurred and mapped out the faults, helping to prevent accidents accurately in the future. Our study shows that “DeFault” will be a powerful ally in making CCUS safer and more effective, especially for the Illinois Basin Decatur Project. Key Points Faults and fractures introduced by carbon storage can be monitored by passive seismicity DeFault algorithm enables an automatic process for accurate and efficient passive seismic event locating and clustering

58 GEOSCIENCES↗

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

Abstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro - and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity ( π and θ ), and selective pressures (pN/pS and Tajima’s D ) within and fixation indices ( F ST ) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity ( π ) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. Conclusions These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro - and microdiversity across microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

Wind Supply Chain Security: Hardware Enumeration and Analysis

This project, undertaken by Idaho National Laboratory (INL) for the Department of Energy (DOE) Wind Energy Technologies Office (WETO), focused on the enumeration and analysis of six key devices important to wind technologies. The devices analyzed included Beckhoff Bus Terminal Controllers (BK1120 and BC9000), a Beckhoff Economy Built-in Panel PC (CP6231), an N-Tron Managed Industrial Ethernet Switch (711FX3), a Bachmann M1 Gateway, and a Bachmann Smart Power Plant Controller. Device selection was driven by availability and budget constraints, with several components sourced from existing wind farms and others procured through a co-agreement with another WETO-funded project. The project's primary objective was to create a hardware bill of materials (HBOM) for each device, identifying and documenting all components to assess potential security and supply chain risks. A detailed analysis revealed over 750 unique components across the six devices, with 80% successfully identified and accompanied by datasheets. Notably, Texas Instruments emerged as the leading supplier, providing over 16% of the components, followed by ON Semiconductor at 11.3%, Analog Devices at 5.3%, and Renesas Electronics Corp at 4.1%. Other notable vendors included Toshiba Corporation, iC-Haus Corporation, Atmel, Vishay, and STMicroelectronics. The enumeration process involved thorough documentation of each component, including its designation, quantity, identifiers, pin package, description, vendor, model, and country of origin. This process provided valuable insights into the complexity and diversity of the electronic systems within these wind devices. It also highlighted the distinct separation of components between vendors, suggesting a trend of vendor-specific component usage. Key findings from the project emphasized the importance of broadening the scope of vendor analysis in future research to gain a comprehensive understanding of component distribution and commonality. The identification of vendor-specific component usage patterns offers new avenues for research and underscores the significance of continued investigation in this field. Overall, this project provides critical insights into the component composition of wind devices, aiding in the development of improved supply chain management and component sourcing strategies. The results contribute valuable knowledge to the wind technology sector, laying the groundwork for enhanced security and resilience in wind energy systems.

17 - WIND ENERGY↗

Observables for recoil identification in high-definition Gas Time Projection Chambers

Directional detection of nuclear recoils is broadly desirable in nuclear and particle physics. At low recoil energies, this capability may be used to confirm the cosmological origin of a dark matter signal, to penetrate the so-called neutrino floor, or to distinguish between different neutrino sources. Gas Time Projection Chambers (TPCs) can enable directional recoil detection if the readout granularity is sufficiently high, as is the case when micro-pattern gaseous detectors (MPGDs) are utilized. A key challenge in such detectors is identifying and rejecting background electron recoil events caused by gamma rays from radioactive contaminants in the detector materials and the environment. We define new observables that can distinguish electron and nuclear recoils, even at keV-scale energies, based on the simulated ionization's topology. Here we perform a simulation study that shows these observables outperform the traditionally used discriminant, dE/dx, by up to three orders of magnitude. Furthermore, these new observables work well even at ionization energies well below 10keV and remain robust even in the regime where directionality fails.

79 ASTRONOMY AND ASTROPHYSICS↗

Identification of Galaxy–Galaxy Strong Lens Candidates in the DECam Local Volume Exploration Survey Using Machine Learning

We perform a search for galaxy–galaxy strong lens systems using a convolutional neural network (CNN) applied to imaging data from the first public data release of the DECam Local Volume Exploration Survey, which contains ~520 million astronomical sources covering ~4000 deg 2 of the southern sky to a 5σ point–source depth of g = 24.3, r= 23.9, i = 23.3, and z = 22.8 mag. Following the methodology of similar searches using Dark Energy Camera data, we apply color and magnitude cuts to select a catalog of ~11 million extended astronomical sources. After scoring with our CNN, the highest-scoring 50,000 images were visually inspected and assigned a score on a scale from 0 (not a lens) to 3 (very probable lens). We present a list of 581 strong lens candidates, 562 of which are previously unreported. We categorize our candidates using their human-assigned scores, resulting in 55 Grade A candidates, 149 Grade B candidates, and 377 Grade C candidates. We additionally highlight eight potential quadruply lensed quasars from this sample. Due to the location of our search footprint in the northern Galactic cap (b > 10 deg) and southern celestial hemisphere (decl. < 0 deg), our candidate list has little overlap with other existing ground-based searches. Where our search footprint does overlap with other searches, we find a significant number of high-quality candidates that were previously unidentified, indicating a degree of orthogonality in our methodology. We report properties of our candidates including apparent magnitude and Einstein radius estimated from the image separation.

79 ASTRONOMY AND ASTROPHYSICS↗

Synchrotron Photoionization Study of the Diisopropyl Ether Oxidation

Abstract Scientific evidence has shown oxygenates help to reduce dangerous pollutants arising from burning fossil fuel in the automotive sector. For this reason, their use as additives has spread widely. The aim of this work consists in providing a comprehensive identification of the main primary oxidation products of diisopropyl ether (DIPE), one of the most promising among etheric oxygenates. The Cl‐initiated oxidation of DIPE is examinated by using a vacuum ultraviolet (VUV) synchrotron radiation at the Advanced Light Source (ALS) of the Lawrence Berkeley National Laboratory (LBNL). Products are identified on the basis of their mass‐to‐charge ratio, shape of photoionization spectra, adiabatic ionization energies, and chemical kinetic profiles, at three different temperatures (298, 550, and 650 K). Acetone, propanal, propene, and isopropyl acetate have been identified as major reaction products. Acetone is the main primary product. Theoretical calculations using the composite CBS‐QB3 method provided useful tools to validate the postulated reaction mechanisms leading to experimentally observed species. The formation of other species is also discussed.

Giustini, Andrea↗

Identifying human failure events (HFEs) for external hazard probabilistic risk assessment

In recent years, several advancements in nuclear power plant (NPP) probabilistic risk assessment (PRA) have been driven by increased understanding of external hazards, plant response, and uncertainties. However, major sources of uncertainty associated with external hazard PRA remain. One important source is how risk-significant human actions that are carried out to enable plant response and recovery from natural hazards cause the close coupling of physical impacts on plants and overall plant risk during these hazard events. This makes human reliability and human-plant interactions important elements to consider in resolving PRA gaps in external hazards. One of the challenges in considering human response in external hazard probabilistic risk assessment (XHPRA) is that most existing human reliability analysis (HRA) models were not developed for assessing actions outside the control room (termed ex-control room actions) and hazard response. To support this new scope, HRA models will need to be developed or modified to support identification of human activities, causal factors, and uncertainties inherent in external hazard response, thereby providing insights regarding event timing and physical event conditions as they relate to human performance. In this study, there are two main objectives: (1) evaluate the applicability of an existing cognitive-based HRA method, Phoenix, to ex-control room actions, and (2) identify sources of uncertainty to be characterized or reduced in order to make this method suitable for XHPRA. The first step of such work is performed by assessing the suitability of existing HRA methods to support identifying human failure events (HFEs) for human response to flooding hazards. These HFEs are human actions or inactions that are involved in human responses to flooding hazards and could contribute to the loss of a critical function for the plant in the scenario being examined. Here, in this work, decomposition analyses using the cognitive-based Phoenix HRA model are used to identify HFEs. The Phoenix method was found to be suitable for analyzing ex-control room actions as well as identifying specific HFEs and underlying crew failure modes (CFMs). However, the method's suitability for use in ex-control room actions would benefit from expanding the available CFMs to accommodate a larger variety of physical and communication tasks.

42 ENGINEERING↗

Parametric model-order reduction for radiation transport using multi-resolution proper orthogonal decomposition

For parametric high-fidelity simulations, it is often desirable to utilize a reduced-order model (ROM) to emulate, at a reduced computational cost, parametric solutions of the governing partial differential equations (PDEs) for unseen parameter values. One commonly employed option is to utilize a data-driven, projection-based ROM supplemented with subspace identification via proper orthogonal decomposition (POD). POD discovers the ROM subspace by computing the singular value decomposition (SVD) of a set of training data from the full-order model (FOM). In streaming-dominated radiation transport simulations with localized sources, solutions often greatly vary over the spatial domain by many orders of magnitude. In such cases, machine-precision arithmetic can be insufficient to obtain an accurate SVD, resulting in a poorly performing ROM. We present a method called multiresolution POD (mrPOD) that mitigates these inaccuracies. The mrPOD method works by decomposing the spatial domain into regions and performing proper orthogonal decomposition on the training dataset separately in each region. In conclusion, mrPOD is tested on single energy group and multigroup atmospheric shielding transport problems and is shown to outperform classic POD.

42 ENGINEERING↗

Discovery of the lensed quasar eRASS1 J050129.5–073309 with SRG/eROSITA and Gaia

We report the discovery and spectroscopic identification of the bright doubly lensed quasar eRASS1 J050129.5–073309 at redshift z = 2.47, selected from the first all-sky survey of the Spectrum Roentgen Gamma (SRG) eROSITA telescope and the Gaia EDR3 catalog. We systematically searched for extragalactic sources with eROSITA X-ray positions that have multiple Gaia counterparts, and we have started spectroscopic follow-up of the most promising candidates using long-slit spectroscopy with NTT/EFOSC2 to confirm the lens nature. The two images are separated by 2.7", and their average Gaia g-band magnitudes are 16.95 and 17.33. Legacy Survey DR10 imaging and image modeling reveal both the lensing galaxy and tentatively the lensed image of the quasar host galaxy. Archival optical light curves show evidence of a variability time delay, with the fainter component lagging the brighter by about 100 days. The brightness of the fainter image has also decreased by about one magnitude since 2019. This dimming was still obvious at the time of the spectroscopic observations and is probably caused by microlensing. The optical spectroscopic follow-up obtained from NTT/EFOSC2 and the evidence provided by the imaging and timing analysis allow us to confirm the lensed nature of eRASS1 J050129.5–073309.

79 ASTRONOMY AND ASTROPHYSICS↗

Occurrence and molecular characterization of Enterocytozoon bieneusi in wild and domestic animal species in Portugal

Abstract The phylum Microsporidia encompasses a diverse group of obligate, intracellular, and spore-forming organisms able to infect a wide range of animal hosts. Among them, Enterocytozoon bieneusi is the most frequently reported species in humans and animals. Little is known about the presence and epidemiology of E. bieneusi in wildlife. We investigated E. bieneusi occurrence and genetic diversity in wild and domestic mammals, through molecular-detection methods, from different regions across Portugal. A total of 756 samples were collected from 288, 242, and 226 wild carnivores, wild ungulates, and domestic animals, respectively. Overall, eight specimens were E. bieneusi-positive (1.1%, 8/756) obtained from five wild (Iberian lynx, Iberian wolf, red fox, stone marten, and wild boar) and one domestic (sheep) host. Nucleotide sequence analysis identified four genotypes of E. bieneusi, Type IV, Wildboar3, BEB6, and PtEbIX. Three of those genotypes belong to Groups 1 (Type IV and Wildboar3) and 2 (BEB6), which are known to contain genotypes capable of infecting a variety of hosts, including humans, highlighting their public health importance. PtEbIX belongs to the dog-specific Group 11. This study represents the first, largest, and most comprehensive molecular-based epidemiology survey carried out in Portugal in wild and domestic animals to date and the first worldwide identification of E. bieneusi in wolf species. Our study showed that wild carnivores and ungulates may act as reservoirs of zoonotic genotypes of E. bieneusi, establishing their role in maintaining the sylvatic cycle of this parasite while representing a potential source of infection for humans and domestic animals.

Figueiredo, Ana M. (ORCID:0000000226236340)↗

Strong lensing of high-energy neutrinos

Here, we consider the effects of strong gravitational lensing by galaxy-scale deflectors on the observations of high-energy ( E $\gg$ GeV ) neutrinos (HENs). For HENs at cosmological distances, the optical depth for multiple imaging is ~10 –3 , implying that while we do not expect any multiply imaged HENs with present samples, next-generation experiments should be able to detect the first such event. We then present the distribution of expected time delays to aid in the identification of such events, in combination with directional and energy information. In order to assist in the evaluation of HEN production mechanisms, we illustrate how lensing affects the observed number counts for a variety of intrinsic luminosity functions of the source population. Finally, we see that the lensing effects on the cosmic neutrino background flux calculation would be negligible by taking kiloparsec-scale jets as an example.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Data for Comparison of Genotyping Assays for Detection of Targeted CRISPR/Cas Mutagenesis in Highly Polyploid Sugarcane

Sugarcane ( Saccharum spp.) is an important biofuel feedstock and a leading source of global table sugar. Saccharum hybrid cultivars are highly polyploid (2n = 100–130), containing large numbers of functionally redundant hom(e)ologs in their genomes. Genome editing with sequence-specific nucleases holds tremendous promise for sugarcane breeding. However, identification of plants with the desired level of co-editing within a pool of primary transformants can be difficult. While DNA sequencing provides direct evidence of targeted mutagenesis, it is cost-prohibitive as a primary screening method in sugarcane and most other methods of identifying mutant lines have not been optimized for use in highly polyploid species. In this study, non-sequencing methods of mutant screening, including capillary electrophoresis (CE), Cas9 RNP assay, and high-resolution melt analysis (HRMA), were compared to assess their potential for CRISPR/Cas9-mediated mutant screening in sugarcane. These assays were used to analyze sugarcane lines containing mutations at one or more of six sgRNA target sites. All three methods distinguished edited lines from wild type, with co-mutation frequencies ranging from 2% to 100%. Cas9 RNP assays were able to identify mutant sugarcane lines with as low as 3.2% co-mutation frequency, and samples could be scored based on undigested band intensity. CE was highlighted as the most comprehensive assay, delivering precise information on both mutagenesis frequency and indel size to a 1 bp resolution across all six targets. This represents an economical and comprehensive alternative to sequencing-based genotyping methods which could be applied in other polyploid species.

Genomics↗

Comparison of genotyping assays for detection of targeted CRISPR/Cas mutagenesis in highly polyploid sugarcane

Sugarcane (Saccharum spp.) is an important biofuel feedstock and a leading source of global table sugar. Saccharum hybrid cultivars are highly polyploid (2n = 100–130), containing large numbers of functionally redundant hom(e)ologs in their genomes. Genome editing with sequence-specific nucleases holds tremendous promise for sugarcane breeding. However, identification of plants with the desired level of co-editing within a pool of primary transformants can be difficult. While DNA sequencing provides direct evidence of targeted mutagenesis, it is cost-prohibitive as a primary screening method in sugarcane and most other methods of identifying mutant lines have not been optimized for use in highly polyploid species. In this study, non-sequencing methods of mutant screening, including capillary electrophoresis (CE), Cas9 RNP assay, and high-resolution melt analysis (HRMA), were compared to assess their potential for CRISPR/Cas9-mediated mutant screening in sugarcane. These assays were used to analyze sugarcane lines containing mutations at one or more of six sgRNA target sites. All three methods distinguished edited lines from wild type, with co-mutation frequencies ranging from 2% to 100%. Cas9 RNP assays were able to identify mutant sugarcane lines with as low as 3.2% co-mutation frequency, and samples could be scored based on undigested band intensity. CE was highlighted as the most comprehensive assay, delivering precise information on both mutagenesis frequency and indel size to a 1 bp resolution across all six targets. This represents an economical and comprehensive alternative to sequencing-based genotyping methods which could be applied in other polyploid species.

60 APPLIED LIFE SCIENCES↗

Collaborative Research Towards a tonne-scale bolometer-based neutrinoless double beta decay experiment (Final Report)

Cryogenic bolometers are an excellent technology for neutrinoless double beta decay searches owing to their very high energy resolution and potential for high radiopurity. The current most advanced large-scale experiment using these detectors is the Cryogenic Underground Observatory for Rare Events (CUORE). The largest source of background in CUORE is degraded alpha particles, emitted from shallow depths of the detector holders, which can deposit a thermal energy signature similar to neutrinoless double beta decay. To mitigate this background, the CUPID concept (CUORE Upgrade with Particle IDentification) proposes to use scintillating cryogenic detectors. Detecting both the scintillation light and the thermal signal allows discrimination between alpha particle events and beta/gamma events. We report on the design and execution of R&D tests to optimize the design of the single detector module, in particular the scintillation light collection efficiency at cryogenic temperatures.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Demonstration of neutron identification in neutrino interactions in the MicroBooNE liquid argon time projection chamber

A significant challenge in measurements of neutrino oscillations is reconstructing the incoming neutrino energies. While modern fully-active tracking calorimeters such as liquid argon time projection chambers in principle allow the measurement of all final state particles above some detection threshold, undetected neutrons remain a considerable source of missing energy with little to no data constraining their production rates and kinematics. We present the first demonstration of tagging neutrino-induced neutrons in liquid argon time projection chambers using secondary protons emitted from neutron-argon interactions in the MicroBooNE detector. We describe the method developed to identify neutrino-induced neutrons and demonstrate its performance using neutrons produced in muon-neutrino charged current interactions. The method is validated using a small subset of MicroBooNE’s total dataset. The selection yields a sample with 60% of selected tracks corresponding to neutron-induced secondary protons. At this purity, the integrated efficiency is 8.4% for neutrons that produce a detectable proton.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

nmrrr : A Reproducible Workflow for Binning and Visualizing NMR Spectra From Environmental Samples

Nuclear magnetic resonance (NMR) spectroscopy is a useful tool for detection and identification of molecular structural information, with increasing applications in environmental sciences. NMR instrument outputs are however heterogeneous and require extensive post-processing, creating barriers to their use and application by non-specialists. Here, we report on a new open-source R package, nmrrr, that processes and visualizes spectral data obtained from one-dimensional solution-state and solid-state NMR experiments; the package also performs relevant calculations commonly applied in natural organic matter communities, such as computing the relative abundance of various functional groups. We document the package's installation, dependencies, and functions; and provide a standard workflow for processing NMR data. This package is currently available on CRAN and GitHub, and community contributions are welcome.

54 ENVIRONMENTAL SCIENCES↗

Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.

36 MATERIALS SCIENCE↗

Multiple Cases of Bacterial Sequence Erroneously Incorporated Into Publicly Available Chloroplast Genomes

Public sequencing databases are invaluable resources to biological researchers, but assessing data veracity as well as the curation and maintenance of such large collections of data can be challenging. Genomes of eukaryotic organelles, such as chloroplasts and other plastids, are particularly susceptible to assembly errors and misrepresentations in these databases due to their close evolutionary relationships with bacteria, which may co-occur within the same environment, as can be the case when sequencing plants. Here, based on sequence similarities with bacterial genomes, we identified several suspicious chloroplast assemblies present in the National Institutes of Health (NIH) Reference Sequence (RefSeq) collection. Investigations into these chloroplast assemblies reveal examples of erroneous integration of bacterial sequences into chloroplast ribosomal RNA (rRNA) loci, often within the rRNA genes, presumably due to the high similarity between plastid and bacterial rRNAs. The bacterial lineages identified within the examined chloroplasts as the most likely source of contamination are either known associates of plants, or co-occur in the same environmental niches as the examined plants. Modifications to the methods used to process untargeted ‘raw’ shotgun sequencing data from whole genome sequencing efforts, such as the identification and removal of bacterial reads prior to plastome assembly, could eliminate similar errors in the future.

59 BASIC BIOLOGICAL SCIENCES↗