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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Endophyte-Promoted Phosphorus Solubilization in Populus

Phosphorus is an important plant nutrient, but in soils the majority of phosphorus, present in the form of a phosphate, forms metal complexes in soil making it relatively unavailable to plants. Therefore, inorganic phosphate solubilization is an important process of plant growth promotion by plant associated bacteria and fungi. Non nodulating plant species have been shown to thrive in low-nutrient environments, in some instances by relying on plant associated microorganisms called endophytes. These microorganisms live within the plant and help supply nutrients for the plant. Despite their potential enormous environmental importance, there are a limited number of studies looking at the direct molecular impact of phosphate solubilizing endophytic bacteria on the host plant. In this work, we studied the impact of two endophyte strains of wild poplar (Populus trichocarpa) that solubilize phosphate. Using a combination of x-ray imaging, spectroscopy methods, and proteomics we report direct evidence of endophyte-promoted phosphorus uptake in poplar. We found that the solubilized phosphate inside the plant may react and become insoluble again suggesting that the phosphate could be re-released within the plant by endophytes. Using synchrotron x-ray fluorescence spectromicroscopy combined with x-ray absorption near-edge structure, we visualized the nutrient phosphorus inside poplar roots inoculated by the selected endophytes and found the phosphorus in both forms of organic and inorganic phosphates inside the root. Tomography-based root imaging revealed a markedly different root biomass and root architecture for poplar samples inoculated with the phosphate solubilizing bacteria strains. Proteomics characterization on poplar roots coupled with protein network analysis revealed novel proteins and metabolic pathways with possible involvement in endophyte enriched phosphorus uptake. These findings suggest an important role of endophytes for phosphorus acquisition and provide a deeper understanding of the critical symbiotic associations between poplar and the endophytic bacteria.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Isoplethal study of phase formation and morphology in uranium-304L steel via scanning electron microscopy

Understanding the formation of uranium alloys with steel is important to advance nuclear technologies involving U metal fuels and machining U metal, and for nuclear forensics applications. No known phase diagram for the quaternary U-(M = Fe, Ni, Cr) system exists. For this work, we synthesize samples of U-304 L steel (nominal composition 70.1:18.3:10.4 at% Fe:Cr:Ni) across the U composition range 4.45—63.35 at%U by arc melting under inert conditions. Using the binary UFe phase diagram as a reference, we identify four U-steel alloy phases. We find the known U-Fe analogue phases UM 2 and U 6 M, and two low-U composition phases with nominal compositions UM 10 and U 2 M 7 . We apply a correlation length analysis to backscatter scanning electron microscopy images of sectioned and polished cross sections to quantify the domain formation length scale. We demonstrate that these depend heavily on the initial composition and range from 30 nm to 1.5 µm. This result, in particular, could be applicable to theoretical predictions of transport properties. Furthering our understanding of U alloy phase formation with important structural elements such as steel primaries is foundational in developing future nuclear technology.

36 MATERIALS SCIENCE↗
DOE OSTI2023

High-quality RNA extraction and the regulation of genes encoding cellulosomes are correlated with growth stage in anaerobic fungi

Anaerobic fungi produce biomass-degrading enzymes and natural products that are important to harness for several biotechnology applications. Although progress has been made in the development of methods for extracting nucleic acids for genomic and transcriptomic sequencing of these fungi, most studies are limited in that they do not sample multiple fungal growth phases in batch culture. In this study, we establish a method to harvest RNA from fungal monocultures and fungal–methanogen co-cultures, and also determine an optimal time frame for high-quality RNA extraction from anaerobic fungi. Based on RNA quality and quantity targets, the optimal time frame in which to harvest anaerobic fungal monocultures and fungal-methanogen co-cultures for RNA extraction was 2-5 days of growth post-inoculation. When grown on cellulose, the fungal strain Anaeromyces robustus cocultivated with the methanogen Methanobacterium bryantii upregulated genes encoding fungal carbohydrate-active enzymes and other cellulosome components relative to fungal monocultures during this time frame, but expression patterns changed at 24-hour intervals throughout the fungal growth phase. These results demonstrate the importance of establishing methods to extract high-quality RNA from anaerobic fungi at multiple time points during batch cultivation.

Brown, Jennifer L.↗
DOE OSTI2022

Multimodal study of the impact of stimulation pH on shale pore structure, with an emphasis on organics behavior in alkaline environments

The tight nature of shale formations calls for hydraulic fracturing techniques able of altering the pore architecture to facilitate the production of hydrocarbon resources. The composition, pH, salinity, density and chemistry of Hydraulic Fracturing Fluids (HFF) vary substantially depending on reservoir characteristics. pH is among the most important stimulation fluid properties, ranging from very acidic, for carbonate reservoirs, to basic, in the case of clay-rich formations. pH regulates what geochemical reactions take place between the stimulation fluid and shale, as well as pore architecture alteration. The dissolution of carbonates and pyrite, and the precipitation of common minerals such as barite, gypsum and iron oxides in acidic environments have been extensively documented. In contrast, alkali stimulation environments and the role of organic components have received less attention. This research provides insight into the role of both minerals and organic components during alkaline stimulation, and the resulting pore architecture alterations. Here, a set of reactive experiments are performed using three different shales, with varying organic matter (OM) content, at different pH (3, 6, 8, 10, 12). The analysis of pore architecture alteration induced by the reaction was performed via nitrogen (N2) gas adsorption and Time-Domain Nuclear Magnetic Resonance (TD-NMR). Inductively Coupled Plasma - Optical Emission Spectrometry (ICP-OES) was used to measure the composition of the stimulation fluid post-reaction. The system with a larger impact on the pore architecture (pH 12) underwent a more extensive analysis through the application of Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) and x-ray Diffraction (XRD). Results show that mineral dissolution contributed to the creation of secondary porosity, mainly through dissolution of clays and silicates. We show that the abundance and distribution of organic matter both play a significant role in changes in pore architecture. Most samples showed an increase in inter-organic porosity, likely due to the organic acids within kerogen reacting with the stimulation fluid. Samples with a larger amount and more widespread distribution of organic matter show the most significant alterations. Finally, we also highlight the dissolution process of iron-rich minerals, including framboidal pyrite, as another important source of secondary porosity.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2021

Evidence of lithium mobility under neutron irradiation

Understanding the evolution of intermetallic materials in high-radiation environments is of great importance for fusion science and national security. Tritium ( 3 H) and lithium ( 6 Li, 7 Li) transport within neutron irradiated claddings coated with aluminide (FeAl3) has been investigated using state-of-the-art multimodal imaging. Specifically, scanning electron microscopy – focused ion beam (SEM-FIB) was used to prepare irradiated coating lift-out samples for follow-on microanalysis. Here, scanning transmission electron microscopy (STEM) was used to acquire atomic-scale information on the carbonaceous structure and elemental mapping. Atomic force microscopy (AFM) was used to determine lift-out dimensions nondestructively. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) spectral and depth profiling show unexpected lithium isotopic distributions in the irradiated cladding, raising an important evidence of possible light isotope mobility within the cladding under elevated temperature and irradiation. ToF-SIMS three-dimensional chemical mappings of mid- and bottom-cladding coatings show light isotopic (e.g., 3 H, 6 Li, 7 Li) distributions in the irradiated coating and give new insights into the fundamental mechanism related to transport mechanisms within the cladding. Multimodal imaging is power to link microstructure, chemistry, and nanoscale defects that impact reliability of these materials. Furthermore, chemical mapping offers observations of the microstructural evolution due to irradiation and provides insights into unexpected material transport under extreme conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Establishing metrics to quantify spatial similarity in spherical and red blood cell distributions

As computational power increases and systems with millions of red blood cells can be simulated, it is important to note that varying spatial distributions of cells may affect simulation outcomes. Since a single simulation may not represent the ensemble behavior, many different configurations may need to be sampled to adequately assess the entire collection of potential cell arrangements. In order to determine both the number of distributions needed and which ones to run, we must first establish methods to identify well-generated, randomly placed cell distributions and to quantify distinct cell configurations. We utilize metrics to assess (1) the presence of any underlying structure to the initial cell distribution and (2) similarity between cell configurations. We propose the use of the radial distribution function to identify long-range structure in a cell configuration and apply it to a randomly distributed and structured set of red blood cells. To quantify spatial similarity between two configurations, we make use of the Jaccard index, and characterize sets of red blood cell and sphere initializations. As an extension to our work submitted to the International Conference on Computational Science, we significantly increase our data set size from 72 to 1048 cells, include a similar set of studies using spheres, compare the effects of varying sphere size, and utilize the Jaccard index distribution to probe sets of extremely similar configurations. Our results show that the radial distribution function can be used as a metric to determine long-range structure in both distributions of spheres and RBCs. We determine that the ideal case of spheres within a cube versus bi-concave shaped cells within a cylinder affects the shape of the Jaccard index distributions, as well as the range of Jaccard values, showing that both the shape of particle and the domain may play a role. Furthermore, we also find that the distribution is able to capture very similar configurations through Jaccard index values greater than 95% when appending several nearly identical configurations into the data set.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Illitization in the Mt. Simon Sandstone, Illinois Basin, USA: Implications for carbon dioxide storage

Clay mineral cementation is one of the most important controls on sandstone reservoir properties. Here, in this paper, the diagenetic history of the Mt. Simon reservoir complex is studied to reveal the origin, timing, and controls of illitization. Samples of sandstone and shale from Mt. Simon reservoir complex were acquired from the Illinois Basin–Decatur Project (IBDP), a CO 2 storage demonstration project in the central Illinois Basin. Petrographic, SEM, TEM, XRD analyses and K/Ar age dating were completed to identify the major detrital and diagenetic components of the samples and reveal illite to be the major clay component in all samples. Illitic clay coatings in the lower Mt. Simon reservoir are identified as a major control on reservoir properties by inhibiting major precipitation of authigenic quartz during illitization, resulting in highly permeable sandstone, essential for CO 2 storage. The coating box-work morphology and mineralogy are indicative of a detrital smectite origin with subsequent illite growth associated with feldspar dissolution and kaolinite alteration. The mineralogy of bulk material and separate grain size fractions (2–0.6 μm; 0.6–0.2 μm; < 0.2 μm) with illite polytypes 2M 1 , 1M, and 1M d were quantified and age dated via 40 K- 40 Ar methods. The shales or reservoir seals contain the highest proportions of detrital illite with illite in the lower Mt. Simon Sandstone reservoir identified as solely diagenetic. Two major events of illitization are identified throughout the Mt. Simon with more porous reservoir rock exhibiting the older event from approximately 360 to 315 Ma and tighter sandstone units with reservoir properties too low to be considered reservoir exhibiting illite dates from 250 to 220 Ma. This partitioning of illitization is attributed to varied mineralogy controlled by depositional changes and evolution of the greater basin.

58 GEOSCIENCES↗
DOE OSTI2021

New approach to precisely measure γ-ray intensities for long-lived fission products, with results for the decay of 95 Zr

For many fission products, the rays emitted following decay provide an easily-detectable signature that can be used to identify their quantities and distributions in a sample. As a result, γ-ray spectroscopy is often exploited to study fission-product yields, provided sufficiently accurate information on the γ-ray intensity is available. However, in many cases, the uncertainties in the existing nuclear data are large enough that they compromise the precision achievable for modern experiments and applications. To address this need, we have developed a new experimental method that is well suited to precisely measure absolute γ-ray intensities in the β decay of long-lived fission products. The approach involves the production of a radiopure sample by implantation of a mass-separated ion beam from the CAlifornium Rare Isotope Breeder Upgrade (CARIBU) facility on a thin carbon foil. The emitted β-decay radiation is detected with a 4π gas proportional counter and a meticulously efficiency-calibrated high-purity germanium (HPGe) detector. As a first measurement to demonstrate the approach, we studied the absolute γ-ray intensities of the strongest transitions following the β decay of 95 Zr and its decay-daughter 95 Nb, and determined them to fractional precisions of better than 1–2%. In addition, with a larger sample of activity produced through neutron irradiation of an isotopically-enriched Zr foil, we performed a high-precision measurement of the relative γ-ray intensities following the decay of 95 Zr with just the HPGe detector. Here, the sample-production method at CARIBU and the coincidence detection approach demonstrated here can be applied to study fission products with half-lives longer than a day, which includes isotopes important not only for nuclear-energy and national-security applications, but also for medical-isotope research and environmental monitoring.

4π↗
DOE OSTI2024

Modeling performance of data collection systems for high-energy physics

Exponential increases in scientific experimental data are outpacing silicon technology progress, necessitating heterogeneous computing systems—particularly those utilizing machine learning (ML)—to meet future scientific computing demands. The growing importance and complexity of heterogeneous computing systems require systematic modeling to understand and predict the effective roles for ML. We present a model that addresses this need by framing the key aspects of data collection pipelines and constraints and combining them with the important vectors of technology that shape alternatives, computing metrics that allow complex alternatives to be compared. For instance, a data collection pipeline may be characterized by parameters such as sensor sampling rates and the overall relevancy of retrieved samples. Alternatives to this pipeline are enabled by development vectors including ML, parallelization, advancing CMOS, and neuromorphic computing. By calculating metrics for each alternative such as overall F1 score, power, hardware cost, and energy expended per relevant sample, our model allows alternative data collection systems to be rigorously compared. We apply this model to the Compact Muon Solenoid experiment and its planned high luminosity-large hadron collider upgrade, evaluating novel technologies for the data acquisition system (DAQ), including ML-based filtering and parallelized software. The results demonstrate that improvements to early DAQ stages significantly reduce resources required later, with a power reduction of 60% and increased relevant data retrieval per unit power (from 0.065 to 0.31 samples/kJ). However, we predict that further advances will be required in order to meet overall power and cost constraints for the DAQ.

Olin-Ammentorp, Wilkie (ORCID:0000000224729862)↗
DOE OSTI2020

A Thin Alumina Film as a Tritium Adsorption Inhibitor for Stainless Steel 316

The effect of a thin alumina coating on stainless-steel 316 (SS316) samples on tritium adsorption and transport are discussed. Compact films of alumina were produced on the surfaces of pristine SS316 samples using an atomic layer deposition (ALD) technique. Subsequently, these samples were exposed for 24 hours to a deuterium-tritium gas mixture (P T =0.5 atm, 25°C). A combination of methods including selective-etching and programmed thermal desorption were employed to assess both, the depth profile of the tritium concentration in the sample and the total quantity of tritium absorbed respectively. Tritium was quantitatively determined through the measurement of beta radioactivity using liquid-scintillation counting techniques. Data suggest that SS316 with a thin film of alumina reduces the total tritium uptake by ~25% relative to uncoated samples. Significantly, such films appear to reduce, by a factor of 200, tritium diffusion into SS316 and therefore constitute an effective barrier against tritium transport. This observation is of practical importance for tritium and, generally, reactive gas handling.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline

Abstract Genetic stock identification (GSI) is an important fisheries management tool to identify the origin of fish harvested in mixed stock fisheries. Periodic updates of genetic baselines can improve performance via the addition of unsampled or under‐sampled populations and the inclusion of more informative markers. We used a combination of baselines to evaluate how population representation, marker number, and marker type affected the performance and accuracy of genetic stock assignments (self‐assignment, bias, and holdout group tests) for steelhead ( Oncorhynchus mykiss ) in the Snake River basin. First, we compared the performance of an existing genetic baseline with a newly developed one which had a reduced number of individuals from more populations using the same set of markers. Self‐assignment rates were significantly higher ( p < 0.001; +5.4%) for the older, larger baseline, bias did not differ significantly between the two, but there was a significant improvement in performance for the new baseline in holdout results ( p < 0.001; mean increase of 25.0%). Second, we compared the performance of the new baseline with increased numbers of genetic markers (~2x increase of single‐nucleotide polymorphisms; SNPs) for the same set of baseline individuals. In this comparison, results produced significantly higher rates of self‐assignment ( p < 0.001; +9.7%) but neither bias nor leave‐one‐out were significantly affected. Third, we compared 334 SNPs versus opportunistically discovered microhaplotypes from the same amplicons for the new baseline, and showed the latter produced significantly higher rates of self‐assignment ( p < 0.01; +2.6%), similar bias, but slightly lower holdout performance (−0.1%). Combined, we show the performance of genetic baselines can be improved via representative and efficient sampling, that increased marker number consistently improved performance over the original baseline, and that opportunistic discovery of microhaplotypes can lead to small improvements in GSI performance.

Hargrove, John S.↗
DOE OSTI2023

Building a genome-based understanding of bacterial pH preferences

The environmental preferences of many microbes remain undetermined. This is the case for bacterial pH preferences, which can be difficult to predict a priori despite the importance of pH as a factor structuring bacterial communities in many systems. We compiled data on bacterial distributions from five datasets spanning pH gradients in soil and freshwater systems (1470 samples), quantified the pH preferences of bacterial taxa across these datasets, and compiled genomic data from representative bacterial taxa. While taxonomic and phylogenetic information were generally poor predictors of bacterial pH preferences, we identified genes consistently associated with pH preference across environments. We then developed and validated a machine learning model to estimate bacterial pH preferences from genomic information alone, a model that could aid in the selection of microbial inoculants, improve species distribution models, or help design effective cultivation strategies. More generally, we demonstrate the value of combining biogeographic and genomic data to infer and predict the environmental preferences of diverse bacterial taxa.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Oxidized structure and Compositional properties of 1144 phase FBS by analytical electron microscopy

The 1144 phase (Ae1A1Fe4As4) shows a strong advantage of engineering fabrication among Fe Iron)-based superconductor (FBS) family due to the robustness of its superconducting properties with respect to chemical inhomogeneities, granted by its uniform crystalline-layered structure. This regularity is furthermore associated to crystalline defects capable of acting as efficient pinning centers, which high critical currents achieved at high fields for these superconductors. Like other FBS phases, its lossless current-carrying capability can be remarkably degraded by distractions at grain boundaries (GBs). GB oxidation is an issue of upmost importance to the realization of the practical FBS application for high field (> 20T) magnet. In this study, we explore oxidized grain boundary and intrinsic grain structural properties of 1144 polycrystalline samples by applying analytical electron microscopy such as atomic resolution scanning transmission electron microscopy and atom probe tomography. These structural properties of samples produced by a mechanochemically assisted synthesis are evaluated following the degradation of superconducting properties due to oxidation. We observe a strong correlation between the contamination at grain boundaries and the decrease of transport properties of the bulk sample, while the crystallin structure seems to be not affected by the oxidation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

First Report and Molecular Variability of Belonolaimus longicaudatus Associated with Turfgrass in Maryland

Abstract Turfgrass is a crop used extensively in athletic fields and golf courses in Maryland. A soil sample collected in July 2023 from an athletic field in Baltimore County, Maryland, part of a turfgrass nematode survey, containedBelonolaimus longicaudatus. In the southeastern United States,B. longicaudatusis an economically important pathogen of warm season turfgrass. The density was four individuals/100 cm 3 of soil, and no visual symptoms were observed in the bermudagrass field. Morphological features and morphometrics of males and females were consistent withB. longicaudatusand placed the Maryland population in a subclade that was geographically represented by populations from north and west Florida, Texas, and South Carolina. Sequencing of the internal transcribed spacer region ITS1 and ITS2 and 28S large ribosomal subunit D2-23 expansion region confirmed the species' identity. Phylogenetic trees and parsimony network analysis placed the Maryland isolate in a large grouping ofB. longicaudatuspopulations including those from Alabama, Delaware, Florida, Indiana, Mississippi, South Carolina, and Texas. To our knowledge, this is the first report ofB. longicaudatusin Maryland.

Zoology↗
DOE OSTI2022

Stellar Abundance Maps of the Milky Way Disk

To understand the formation of the Milky Way's prominent bar it is important to know whether stars in the bar differ in the chemical element composition of their birth material as compared to disk stars. This requires stellar abundance measurements for large samples across the Milky Way's body. Such samples, e.g., luminous red giant stars observed by the Sloan Digital Sky Survey's APOGEE survey, will inevitably span a range of stellar parameters; as a consequence, both modeling imperfections and stellar evolution may preclude consistent and precise estimates of their chemical composition at a level of purported bar signatures, which has left current analyses of a chemically distinct bar inconclusive. Here, we develop a new self-calibration approach to eliminate both modeling and astrophysical abundance systematics among red giant branch (RGB) stars of different luminosities (and hence surface gravity $\mathrm{log} g$). We apply our method to 48,853 luminous APOGEE Data Release 16 RGB stars to construct spatial abundance maps of 20 chemical elements near the Milky Way's mid-plane, covering galactocentric radii of 0 kpc < R GC < 20 kpc. Our results indicate that there are no abundance variations whose geometry matches that of the bar, and that the mean abundance gradients vary smoothly and monotonically with galactocentric radius. We confirm that the high-α disk is chemically homogeneous, without spatial gradients. Furthermore, we present the most precise [Fe/H] versus R GC gradient to date with a slope of – 0.057 ±0.001 dex kpc –1 out to approximately 15 kpc.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Decreasing wind speed extrapolation error via domain-specific feature extraction and selection

Abstract. Model uncertainty is a significant challenge in the wind energy industry and can lead to mischaracterization of millions of dollars' worth of wind resources. Machine learning methods, notably deep artificial neural networks (ANNs), are capable of modeling turbulent and chaotic systems and offer a promising tool to produce high-accuracy wind speed forecasts and extrapolations. This paper uses data collected by profiling Doppler lidars over three field campaigns to investigate the efficacy of using ANNs for wind speed vertical extrapolation in a variety of terrains, and it quantifies the role of domain knowledge in ANN extrapolation accuracy. A series of 11 meteorological parameters (features) are used as ANN inputs, and the resulting output accuracy is compared with that of both standard log-law and power-law extrapolations. It is found that extracted nondimensional inputs, namely turbulence intensity, current wind speed, and previous wind speed, are the features that most reliably improve the ANN's accuracy, providing up to a 65 % and 52 % increase in extrapolation accuracy over log-law and power-law predictions, respectively. The volume of input data is also deemed important for achieving robust results. One test case is analyzed in depth using dimensional and nondimensional features, showing that the feature nondimensionalization drastically improves network accuracy and robustness for sparsely sampled atmospheric cases.

17 WIND ENERGY↗
DOE OSTI2020

Host-specific and tissue-dependent orchestration of microbiome community structure in traditional rice paddy ecosystems

Abstract Background and aim Rice and duckweed are two monocotyledonous plants that naturally coexist in paddy fields. While the presence of duckweed in paddy fields significantly improves rice productivity, the interplay between soil microbes and the two plant hosts in this agroecosystem remains unexplored. Methods We compared the bacterial community structure between duckweed, rice and soil from multiple rice paddies. We also isolated bacteria from these communities and characterized their modes of bacterial colonization and plant growth-promotion using model plants. Results Our data indicate that host-specific and tissue-dependent factors reproducibly orchestrate the bacterial community structure associated with their plant hosts. This is corroborated by results from culture-dependent approaches in which the dominant genus Pantoea isolated from rice aerial tissues can strongly attach and colonize gnotobiotic duckweed in spite of the low representation of this bacterial genus in the natural duckweed microbiome. Our study identified a core of 254 bacterial taxa that are consistently found in all rice and duckweed tissue samples from rice paddy fields. Furthermore, characterizing auxin-producing bacteria isolates from both plant species identified potential plant growth-promoting bacteria that may improve growth for both duckweed and rice in paddy fields. Conclusions Results from this work provide evidence for the importance of the host tissue and species context in determining plant colonization by microbes in the paddy field system. The resources generated in this study could facilitate the agronomic deployment of microbes for more sustainable rice production.

Agriculture↗
DOE OSTI2023

Virulence factors and antimicrobial resistance profiles of Campylobacter isolates recovered from consecutively reused broiler litter

ABSTRACT Campylobacterinfections are a leading cause of bacterial diarrhea in humans globally. Infections are due to consumption of contaminated food products and are highly associated with chicken meat, with chickens being an important reservoir forCampylobacter. Here, we characterized the genetic diversity ofCampylobacter jejuni(C. jejuni) andCampylobacter coli(C. coli) detected in broiler chicken litter over three consecutive flocks and determined their antimicrobial resistance (ARM) and virulence factor (VF) profiles.Campylobacterwas detected in 9.38% (27/288) of litter samples collected. Antimicrobial susceptibility testing and whole genome sequencing were performed onC. jejuni(n= 39) andC. coli(n= 5) isolates.Campylobactervirulence factors differed within and across broiler houses but were explained by the broiler flock cohort raised on litter,Campylobacterspecies andCampylobactermultilocus sequence type (MLST). Virulence factors involved in the ability to invade and colonize host tissues and evade host defenses were present inC. jejuniisolates (ST-464) from flock cohorts 1 and 2 but absent inC. jejuniisolates (ST-48) from flock cohort 3.C. jejuniisolates from house three harbored a significantly higher proportion of virulence genes with functions related to glycosylation and immune evasion thanC. jejuniisolates from houses 1 and 2 (P< 0.01). AllC. jejuniisolates were susceptible to all antibiotics tested whileC. coli(n= 4) were resistant to tetracycline and harbored the tetracycline resistant ribosomal protection protein (TetO). Our results suggest that house environment and broiler management practices imposed selective pressures on virulence factors and antimicrobial resistance genes ofCampylobacter. IMPORTANCE Campylobacteris a leading cause of foodborne illness in the United States due to consumption of contaminated or mishandled food products, often associated with chicken meat.Campylobacteris common in the microbiota of avian and mammalian gut; however, acquisition of antimicrobial resistance genes (ARGs) and virulence factors (VFs) may result in strains that pose significant threat to public health. Although there are studies investigating the genetic diversity ofCampylobacterstrains isolated from post-harvest chicken samples, there are limited data on the genome characteristics of isolates recovered from preharvest broiler production. Here, we show thatCampylobacter jejuniandCampylobacter colidiffer in their carriage of antimicrobial resistance and virulence factors may also differ in their ability to persist in litter during consecutive grow-out of broiler flocks. We found that presence/absence of virulence factors needed for evasion of host defense mechanisms and gut colonization played an integral role in differentiatingCampylobacterstrains.

Microbiology↗