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At least 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Collisionless Larmor coupling and blob formation in a laser-plasma expanding into a magnetized ambient plasma

Collisionless Larmor coupling is a fundamental process in space and astrophysical plasmas that enables momentum transfer between an expanding plasma and a magnetized ambient medium. Here, in this paper, we report on the laboratory experimental study of Larmor coupling leading to the formation of a plasma blob associated with a laser-driven, super-Alfvénic plasma flow on the Large Plasma Device at the University of California, Los Angeles. The high-repetition rate enables systematic spatial and temporal scans of the plasma evolution using Doppler spectroscopy, as well as measurements of the magnetic field, electrostatic field, and self-emission of both debris and ambient ions using filtered imaging. We observe the self-focusing of the laser-produced plasma and the formation of a secondary diamagnetic cavity associated with a blob composed of background ions. Doppler spectroscopy reveals the transverse velocity distribution of the background ions, providing direct evidence of ion energization via Larmor coupling. The systematic spatial and temporal scans enabled by the high-repetition-rate experiment allow for a detailed characterization of the ion dynamics. These experimental observations are supported by numerical simulations that provide more insight into the kinetic-scale physics associated with blob formation as well as the role of the ambient plasma density.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Effects of Metal and Metal Ion on Biomethane Productivity during Anaerobic Digestion of Dairy Manure

To overcome major limiting factors of microbial processes in anaerobic digestion (AD), metal and metal ions have been extensively studied. However, there is confusion about the effects of metals and metal ions on biomethane productivity in previous research. In this study, Zn and Zn 2+ were selected as representatives of metals and metal ions, respectively, to investigate the effects on biomethane productivity. After the metals and metal ions at different concentrations were added to the batch AD experiments under the same mesophilic conditions, a Zn dose of 1 g/L and a Zn 2+ dose of 4 mg/L were found to cause the highest biomethane production, respectively. The results indicate that metal (Zn) and metal ion (Zn 2+ ) have different mechanisms to improve AD performance. There may be two possible explanations. To act as conductive materials in interspecies electron transfer (IET), relatively high doses of metals (e.g., 1 g/L of Zn, 10 g/L of Fe) are needed to bridge the electron transfer from syntrophic bacteria to methanogenic archaea in the AD process. As essential mineral nutrients, the AD system requires relatively low doses of metal ions (e.g., 4 mg/L of Zn 2+ , 5 mg/L of Fe 2+ ) to supplement the component of various enzymes that catalyze anaerobic reactions and transformations. This research will provide clear insight for selecting appropriate amounts of metals or metal ions to enhance biomethane productivity for industrial AD processes.

09 BIOMASS FUELS↗
DOE OSTI2021

Process intensification of CO 2 capture by low-aqueous solvent

Low-energy solvent-based CO 2 absorption processes have drawn attention as a next-generation post-combustion CO 2 capture technology to reduce CO2 emissions from fossil fuel– or biomass-fired power generation and industrial flue gas streams. A low-aqueous (or water-lean) solvent process may substantially reduce the thermal energy consumption for solvent regeneration. Low-aqueous solvent–based processes are thermally sensitive, requiring a delicate temperature control within the absorber because of the fast exothermic amine-CO 2 reaction and low heat capacity organic diluent. This reaction may result in heat accumulation in a packed absorption column and undesirable CO 2 desorption occurring as the solvent moves through the column, reducing the solvent’s CO 2 capture efficiency if its temperature is not controlled. Using a 3D printed intensified packing device, enhanced heat and mass transfer were demonstrated in an amine-CO 2 scrubbing process using low-aqueous solvent. The multifunctional intensified device facilitates contact of the reactive solvent and gas phases in a single stage and heat removal by a cooling fluid flowing through channels in the interior of the corrugated plates of the device. These functionalities led to effective thermal management along the column via intrastage cooling and significant improvement in CO 2 uptake under a wide range of operating conditions. Intrastage cooling effectively reduced the solvent average temperature along the column by ~10 °C and, as a result, the solvent’s capture efficiency improved by up to 25%.

42 ENGINEERING↗
DOE OSTI2022

Nonradiative Recombination via Charge-Transfer-Exciton to Polaron Energy Transfer Limits Photocurrent in Organic Solar Cells

Here, a recombination and exciton loss mechanism is reported in organic solar cells involving energy transfer between charge transfer (CT) excitons and polarons, impacting photocurrent generation, particularly in the near-infrared where polaronic transitions typically reside. This process sets a low-energy cut-off in the external quantum efficiency spectrum of an excitonic donor/acceptor interface, determined by the low-energy polaron absorption peak and the CT state reorganization energy. Furthermore, this process explains the deviation from unity and bias dependence of the CT state's internal quantum efficiency at low photon energies. This process is demonstrated in a variety of systems and it is hypothesized that CT state to polaron energy transfer recombination may be responsible for a share of nonradiative recombination in all organic photovoltaics and can explain numerous experimentally observed device trends regarding photocurrent generation and energy losses. Overall, this work enhances the understanding of photophysical processes in organic materials and allows the design of systems that can avoid this recombination pathway.

14 SOLAR ENERGY↗
DOE OSTI2026

Optimal Design and Techno-Economic Analysis of 3D-Printed, Intensified Packings for Absorbers and Strippers in Solvent-Based CO 2 Capture

A potential technology for the CO 2 absorption process is utilizing intensified structured packing with embedded cooling/heating channels for continuous heat exchange, which can overcome limitations of discrete methods, such as discrete intercooling and centralized reboilers, to aid in reducing energy consumption and decreasing costs. This work investigates the modeling of intensified packing (IP) for the stripper tower, extending on previous work for the absorber, which distributes heat internally within the column, improving the thermodynamics for the solvent regeneration process. The model includes submodels for steam turbine extraction to produce steam at various qualities as well as a surrogate model for calculating steam enthalpy. A cost model for a plant-scale absorption capture process was developed, allowing for the design of the plant to be optimized, subject to minimizing capture cost using two different power plant flue gas sources. In this optimization, the placement of IP in both towers is optimized to balance the trade-off between enhanced heat transfer and reduced mass transfer volume. For natural gas combined cycle flue gas, the standard process configuration had a minimum cost of $\$$65.40/tonne CO 2 , and considering IP, the minimum capture cost is reduced to $\$$62.73/tonne, with utilization in the stripper column, which reduces yearly costs by up to $\$$2.67 MM/yr. Cooling the absorber through IP, or intercoolers, was only found to be beneficial at higher capture rates, with IP in both towers having a cost of capture of $\$$68.08/tonne at 99.9% capture, a reduction of $\$$12.64/tonne when using only intercoolers at the same capture rate. When capturing from pulverized-coal power plants, the minimum cost of capture when using IP in both towers is $\$$44.18/tonne (at 97% capture), while the standard configuration with and without intercoolers was $\$$45.69 and $\$$47.22 per tonne, respectively. This results in a reduction in yearly costs of $\$$16.98 MM/yr from the base-case configuration. At this higher CO 2 concentration, cooling in the absorber from the IP becomes extremely beneficial, reducing energy consumption by up to 6%.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2020

Extracting capture from transfer reactions

Indirect reaction techniques are very important in astrophysics as they provide information that is complementary to direct measurements or that otherwise cannot be obtained directly. It is then critical to have a reliable reaction theory that can connect the reaction measurement with the astrophysical information desired. This is a brief report on the progress made in the theory for transfer reactions when used to determine neutron capture rates for r-process and proton capture for rp-process nuclei. We will discuss the different types of experiments and their connection to astrophysics. An overview of the current status of the theory will be provided, with emphasis on several recent theory developments, including transfer to continuum, the improvement of the optical potential and uncertainty quantification. Applications to a couple of neutron rich and proton rich cases will be discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Catalytic Bio-crude Production in a Novel, Short-Contact Time Reactor

RTI has developed a catalytic fast pyrolysis (CFP) process to produce biomass-based hydrocarbon replacement fuels. From a technology perspective, this advanced biofuels process produces liquid transportation fuels that can leverage capital expenditures in the existing petroleum distribution infrastructure. From a business perspective, this technology does not face potential market limitations caused by oxygenate blend limitations for light duty vehicle applications. A promising catalyst has been developed with excellent potential for deoxygenation to produce a hydrocarbon-rich biocrude that is more suitable for upgrading with traditional hydroprocessing technology. The role of the catalyst is to control the chemistry during biomass pyrolysis to produce a biocrude in a single step that has lower oxygen content and is more thermally stable than conventional biomass fast pyrolysis oil. Catalyst properties are optimized to minimize gas and coke production and improve catalytic deoxygenation and biocrude yields. Results from this project have demonstrated that biocrudes from catalytic fast pyrolysis contain <20 wt% oxygen, with the organic fraction as low as 12% oxygen. These oxygen numbers are > 50% lower compared to traditional fast pyrolysis oils. The biocrude produced from our CFP process can be upgraded to gasoline range hydrocarbons. A very conservative approach for upgrading included a preliminary stabilization step followed by a hydroprocessing step. The oxygen content in the upgraded product was decreased by 97% (to less than 3wt %) from the oxygen content of the biocrude sample. Additionally, the acid content was reduced by 99% from the acid content of the biocrude sample. In an optimized integrated process, the CFP step and the hydroprocessing (upgrading) step need to be carefully balanced to maximize the input biomass energy that is recovered in the finished biofuels. Hydrogen utilization and carbon recovery during both catalytic biomass pyrolysis and biocrude upgrading need to be optimized to maximize energy recovery in the finished biofuel. A nominal 1 ton per day (TPD) catalytic biomass pyrolysis system was designed based on the laboratory experimental data. The system was designed to achieve the short residence times (0.5–2 sec) and high heat transfer rates required for maximum liquid biocrude yields while optimizing process integration to maintain catalyst activity by continuous regeneration. The catalytic biomass pyrolysis reactor is a continuously circulating single-loop transport reactor design that is flexible enough to allow sensitivity studies around temperature, residence time, biomass feed rate, and catalyst-to-biomass ratio (i.e., catalyst circulation rate) for process optimization. For a nominal 100 lb/hr feed rate of dry biomass, the products include ~25 lb/hr char and coke, ~20 lb/hr permanent gases, and ~55 lb/hr condensable vapors. Pyrolysis temperatures are 350–600°C, and the system is operated close to ambient pressure. Production of the catalyst developed within the project was scaled up to provide enough material (200kg) for bench-scale testing. The 1TPD bench-scale unit was fabricated, installed and commissioned with this project. Biocrude samples from wood were produced in this unit with the CFP catalyst with material balance > 90%. The intermediate biocrude yields and chemical composition compare well with previous laboratory results and a hydroprocessing strategy for upgrading the resulting biocrude was developed. The experimental results obtained within this project were used to develop a process model for a 2000 TPD commercial facility. Detailed flow sheets were developed for all major unit operations in the process and provided a basis for an economic analysis to develop capital and operating costs. Estimates of the biofuel production costs were used to develop internal rates of return for the yields and compositions measured for the current state of technology at the end of this project and for the yields anticipated for an optimized (nth plant) scenario as additional process improvements are made.

09 BIOMASS FUELS↗
DOE OSTI2021

Catalysts by pyrolysis: Direct observation of chemical and morphological transformations leading to transition metal-nitrogen-carbon materials

Transition metal-nitrogen-carbon materials (M-N-C catalysts) are promising electrocatalysts in polymer electrolyte fuel cells (PEFCs) and electrolyzer applications. High temperature treatment in inert atmosphere (pyrolysis) is the essential, most common method for the synthesis of M-N-C catalysts and critical to achieve high electrocatalytic activity and electronic conductivity. To this day, despite many uses and successful implementations in materials manufacturing, pyrolysis has been an entirely empirical technology, with process control and optimization relying exclusively on “Edisonian” approach. The knowledge gap in the mechanism about how the precursor is being transformed into catalysts hinders further development of the M-N-C catalysts regardless of the precursor class and processing protocols. In this work, we probed the morphological evolution and chemical transformation of a nitrogen-containing charge transfer organic salt, mixed with transition metal (iron) salt and amorphous silica powder (precursor) during the pyrolysis process via a combination of in situ synchrotron and laboratory-based diagnostic techniques. The pyrolysis process is found to be divided into three stages. During a controlled temperature ramp, the selected organic N-C precursor (nicarbazin) began melting and decomposing just below 400 °C, forming a certain number of micrometer-scale pores and pathways. With increase in temperature from 400 °C to 900 °C, amorphous carbon domains started forming, and reduced (metallic) iron nanoclusters appeared, being dispersed uniformly throughout the carbonaceous matrix. When temperature advanced above 900 °C, graphitization of carbon commenced, associated with appearance and evolution of atomically dispersed metal-nitrogen moieties in the carbonaceous matrix. As the graphitization advanced further, a secondary process of agglomeration of metal nanoparticles occurred. Multi-analytical technique observations conducted here provide a base for rational design and optimization of M-N-C electrocatalysts via pyrolysis.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Modeling the Destruction of Glycolate in the Defense Waste Processing Facility (DWPF) Recycle Stream and Concentration Factors for Glycolate in the 2H Evaporator

Two models were developed to predict maximum glycolate concentrations in the Savannah River Site (SRS) Concentration, Storage, and Transfer Facility (CSTF) from implementation of the Nitric-Glycolic flowsheet at the Defense Waste Processing Facility (DWPF). One model describes the kinetics of glycolate destruction via chemical oxidation with sodium permanganate. This model conservatively predicts glycolate concentration delivered to the CSTF with a high probability the actual glycolate concentration is lower than predicted. The second model describes the potential concentration of said residual glycolate within the 242-16H (i.e., “2H”) Evaporator system.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Understanding interfacial crystallization dynamics on carbon fiber reinforced polypropylene composite manufacturing

Reinforcing polymers with discontinuous fibers improves mechanical properties, such as strength and stiffness, and in some cases achieve isotropic properties, rendering them suitable for various engineering applications. Matrix materials are generally highly engineered thermosets (e.g. crosslinked epoxies), bonded to the fiber periphery by proprietary surface and sizing chemistries. Semicrystalline thermoplastic matrices are less utilized due to poor fiber-matrix bonding resulting in inefficient interfacial load-transfer in reinforced composites. However, flexibility with melt-processing or molding conditions can be leveraged to promote non-covalent interfacial bonding between matrix and fiber via crystallization of the matrix onto fiber surface. In the present study, we utilize a co-mingle chopped carbon and isotactic polypropylene fibers to form isotropic composites, tailoring interfacial immobilized matrix or interphase morphology to optimize performance through precise control of thermal processing/molding windows. Calorimetry and optical microscopy were employed to investigate the impact of carbon fiber at various volume fractions (10, 20, and 30 %) on isotactic polypropylene crystallization and mechanical performance. Variations in mechanical properties correspond to the structural evolution of the interfacial region and are correlated to underlying microstructural attributes using wide-angle X-ray scattering, thermal analysis, and low-field nuclear magnetic resonance spectroscopy. These results provide a practical framework for the manufacturing of thermoplastic matrix composites. In conclusion, the results presented provide a guide for the strategic optimization of interphase design, showcasing tailorable tensile strengths which outperform any isotactic polypropylene carbon fiber composites previously reported in literature.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Fast Charge Induced Phase Evolution and Element Contribution of Nickel-Rich Layered Cathode for Lithium-Ion Batteries

In nickel-rich layered cathode materials, three transition metals (TM = Ni, Co and Mn) play critical roles in Li storage performance. However, rate-dependent phase evolution and elemental contribution of nickel-rich cathode materials are not well understood, but very important for further design and development of these cathodes in high-power applications. Here, the rate-dependent phase evolution and elemental contribution of LiNi 0.5 Mn 0.3 Co 0.2 O 2 (NMC532) cathode are investigated thoroughly by using time-resolved synchrotron-based in situ X-ray diffraction and absorption techniques. The increase of Ni content in NMC532 has been found to be the main cause of the complex structural changes, resulting in distortion of TM-O 6 octahedron and strong static vibration between TM and O coordination. It is revealed that the fast charge (10C and 30C) of NMC532 leads to intermediate Li-poor phases, shrinking of H2 phase region, and prolonged O1 phase. During high-rate charging, Co is oxidized easily in low voltage region, while Ni mainly dominates charge compensation in high voltage region. It is found that delithiation-induced local structure distortion transfers from Ni to Co sites in fast kinetic process. In conclusion, these findings provide in-depth understanding for the fast charge behavior of Ni-rich layered cathode materials and help to guide further development of advanced high-power lithium-ion batteries.

25 ENERGY STORAGE↗
DOE OSTI2020

Structure and Reactivity of Single-Site Vanadium Catalysts Supported on Metal–Organic Frameworks

Single-site catalysts with active species anchored over metal–organic framework (MOF) supports have garnered significant interest in recent years. Catalysts with vanadium oxide (VO x ) species immobilized over Zr-NU-1000 and Hf-MOF-808 (which have nodes containing six Zr (IV) or Hf (IV) ions, respectively) were recently characterized experimentally and were reported to be active for the selective oxidation of benzyl alcohol to benzaldehyde. Here, we report a detailed computational investigation of these VO x -incorporated MOF catalysts (V-MOF) by employing density functional theory. Based on the mode of VO x attachment, various structures are explored, and their relative stabilities and computed IR spectral features are reported. Mechanisms for the selective oxidation reaction are investigated. The analysis of electron flow in the turnover-limiting C–H activation step shows that the hydrogen-atom abstraction process involves a concerted proton-coupled electron-transfer mechanism. Here, the results of this study suggest that in addition to the identity of the metal in the node, the MOF node architecture plays a crucial role in driving the catalytic activities of V-MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Multiscale Temporal Variability of the Global Air‐Sea CO 2 Flux Anomaly

Abstract The global air‐sea CO 2 flux (F) impacts and is impacted by a plethora of climate‐related processes operating at multiple time scales. In bulk mass transfer formulations, F is driven by physico‐ and bio‐chemical factors such as the air‐sea partial pressure difference (∆pCO 2 ), gas transfer velocity, sea surface temperature, and salinity–all varying at multiple time scales. To de‐convolve the impact of these factors on variability in F at different time scales, time‐resolved estimates of F were computed using a global data set assembled between 1988 and 2015. The F anomalies were defined as temporal deviations from the 28‐year time‐averaged value. Spectral analysis revealed four dominant timescales of variability in F–subseasonal, seasonal, interannual, and decadal with relative amplitude differences varying across regions. A second‐order Taylor series expansion was then conducted along these four timescales to separate drivers across differing regions. The analysis showed that on subseasonal timescales, wind speed variability explains some 66% of the global F anomaly and is the dominant driver. On seasonal, interannual, and decadal timescales, the ∆pCO 2 effect controlled by the ∆pCO 2 anomaly, explained much of the F anomaly. On decadal timescales, the F anomaly was almost entirely governed by the ∆pCO 2 effect with large contributions from high latitudes. The main drivers across timescales also dominate the regional F anomaly, particularly in the mid‐high latitude regions. Finally, the driver of the ∆pCO 2 effect was closely connected with the relative strength of atmospheric pCO 2 and the nonthermal component of oceanic pCO 2 anomaly associated with dissolved inorganic carbon and alkalinity.

Environmental Sciences & Ecology↗
DOE OSTI2021

Methane-derived carbon flows into host–virus networks at different trophic levels in soil

Significance The impact of soil viruses on prokaryotic hosts and their functional processes is largely unknown. While metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts, this does not necessarily identify contemporary interactions. To enable a detailed analysis of active virus–host interactions between individual populations, we focused on the critical biogeochemical process of methane (CH 4 ) oxidation and followed the transfer of carbon from hosts to their associated viruses in situ. Analysis of 13 C-enriched metagenomic DNA demonstrated that CH 4 -derived carbon is transferred into viral biomass via both primary and secondary utilizers of CH 4 and suggests viral predation is an important mechanism for releasing CH 4 -derived organic carbon into the soil matrix.

Lee, Sungeun↗
DOE OSTI2023

Can we observe the ion-neutral drift velocity in prestellar cores?

Given the low-ionization fraction of molecular clouds, ambipolar diffusion is thought to be an integral process in star formation. However, chemical and radiative-transfer effects, observational challenges, and the fact that the ion-neutral drift velocity is inherently very small render a definite detection of ambipolar diffusion extremely non-trivial. Here, we study the ion-neutral drift velocity in a suite of chemodynamical, non-ideal magnetohydrodynamic (MHD), two-dimensional axisymmetric simulations of prestellar cores where we alter the temperature, cosmic-ray ionization rate, visual extinction, mass-to-flux ratio, and chemical evolution. Subsequently, we perform a number of non-local thermodynamic equilibrium (non-LTE) radiative-transfer calculations considering various idealized and non-idealized scenarios in order to assess which factor (chemistry, radiative transfer, and/or observational difficulties) is the most challenging to overcome in our efforts to detect the ion-neutral drift velocity. We find that temperature has a significant effect in the amplitude of the drift velocity with the coldest modelled cores (T = 6 K) exhibiting drift velocities comparable to the sound speed. Against expectations, we find that in idealized scenarios (where two species are perfectly chemically co-evolving) the drift velocity ‘survives’ radiative-transfer effects and can in principle be observed. However, we find that observational challenges and chemical effects can significantly hinder our view of the ion-neutral drift velocity. Finally, we propose that HCN and HCNH + ⁠, being chemically co-evolving, could be used in future observational studies aiming to measure the ion-neutral drift velocity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Real-Time High-Accuracy Digital Wireless Time, Frequency, and Phase Calibration for Coherent Distributed Antenna Arrays

his work presents a fully-digital high-accuracy real-time calibration procedure for frequency and time alignment of open-loop wirelessly coordinated coherent distributed antenna array (CDA) modems, enabling radio frequency (RF) phase coherence of spatially separated commercial off-the-shelf (COTS) software-defined radios (SDRs) without cables or external references such as the global navigation satellite system (GNSS). Building on previous work using high-accuracy spectrally-sparse time of arrival (ToA) waveforms and a multistep ToA refinement process, a high-accuracy two-way time transfer (TWTT)-based time–frequency coordination approach is demonstrated. Due to the two-way nature of the high-accuracy TWTT approach, the time and frequency estimates are Doppler and multipath tolerant, so long as the channel is reciprocal over the synchronization epoch. This technique is experimentally verified using COTS SDRs in a lab environment in static and dynamic scenarios and with significant multipath scatterers. Time, frequency, and phase stability were evaluated by beamforming over coaxial cables to an oscilloscope which achieved time and phase precisions of ~60– 70 ps , with median coherent gains above 99% using optimized coordination parameters, and a beamforming frequency root-mean-square error (RMSE) of 3.73 ppb in a dynamic scenario. Finally, experiments were conducted to compare the performance of this technique with previous works using an analog continuous-wave two-tone (CWTT) frequency reference technique in both static and dynamic settings.

Clock synchronization↗
DOE OSTI2026

ML–Enabled FPGA Framework for Fast Quantum State Discrimination in Mid-Circuit Measurement Regimes

Accurate and low-latency quantum state discrimination is essential for protocols involving mid-circuit measurement (MCM) and conditional feed-forward. In superconducting quantum systems, conventional readout pipelines transfer measurement data to host processors for post-processing, introducing millisecond-scale delays that far exceed qubit coherence times. To overcome this bottleneck, we present an in-situ machine learning (ML) inference engine implemented on an FPGA for real-time quantum state discrimination. Our design performs inference directly on digitized readout signals with 40 ns latency, supports both qubit and qutrit readout, and enables conditional operations without host-side intervention. This capability is critical for MCM and for feedback-driven protocols such as quantum error correction. We validate the system on superconducting transmon hardware, demonstrating robust discrimination fidelity across multiple qubit and qutrit channels. We further demonstrate conditional qutrit logic driven by FPGA-resident classification, highlighting the potential of low-latency ML-on-FPGA control for NISQ applications and scalable fault-tolerant quantum computing.

Vora, Neel [Lawrence Berkeley National Laboratory ↗
DOE OSTI2021

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

Background Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context. Results. Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. Conclusions The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗