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DOE OSTI2023

High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration

Efficient genome engineering is critical to understand and use microbial functions. Despite recent development of tools such as CRISPR-Cas gene editing, efficient integration of exogenous DNA with well-characterized functions remains limited to model bacteria. Here, we describe serine recombinase–assisted genome engineering, or SAGE, an easy-to-use, highly efficient, and extensible technology that enables selection marker–free, site-specific genome integration of up to 10 DNA constructs, often with efficiency on par with or superior to replicating plasmids. SAGE uses no replicating plasmids and thus lacks the host range limitations of other genome engineering technologies. We demonstrate the value of SAGE by characterizing genome integration efficiency in five bacteria that span multiple taxonomy groups and biotechnology applications and by identifying more than 95 heterologous promoters in each host with consistent transcription across environmental and genetic contexts. We anticipate that SAGE will rapidly expand the number of industrial and environmental bacteria compatible with high-throughput genetics and synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Active populations and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslands

Climate influences soil microbial composition and function, but the relative importance of a site's historic climate versus its more immediate environmental conditions is unclear. Using quantitative stable isotope probing (qSIP), we characterized actively growing soil microbial communities and soil properties in three California annual grasslands that span a rainfall gradient and have developed on similar parent material. The soils were assayed in the wet winter season, when environmental conditions are most similar across sites. Since growing populations might be expected to be most responsive to contemporary environmental conditions, we hypothesized that the structure of growing microbial communities would be more similar across the gradient than that of total communities (i.e., including non-growing populations). In addition, we hypothesized that population growth rates would be slowest in the driest site, reflecting a legacy effect of low soil moisture on microbial growth. Soils along the rainfall gradient differed in pH, texture, and cation exchange capacity, but not in total C, C:N or dominant minerals. The radiocarbon (14C) age of soil C (reflecting turnover time) increased with mean annual precipitation but soil respiration was uniformly modern, reflecting microbial reliance on recent C inputs across the sites. The structure of both total and growing microbial communities differed across sites. Across major microbial phyla, including the Actinobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Proteobacteria, bacterial growth rates were consistently lower in the site with the lowest mean annual precipitation. Taxa that were growing at the dry site alone grew more slowly than taxa that grew at multiple sites. These results reflect the influence of climate history and point to the role of environmental filtering at the driest site in shaping its slower growing microbial community, possibly reflecting adaptation to repeated exposure to water stress. Lastly, across taxa, the growth rate of a taxon at one site was correlated with its growth rate in the other sites. Furthermore, this growth rate coherence is likely a consequence of genetically determined physiological traits and is consistent with the idea that evolutionary history constrains growth rate.

Environmental filtering↗

DOE OSTI2024

Tuning Catalytically Active Single Sites in Nonstoichiometric, Mixed Metal Oxides for Oxygen Electrocatalysis (Final Technical Report)

The objective of the proposed work is to employ controlled synthesis, advanced characterization, detailed electrochemical testing and theoretical calculations to develop a framework that would guide the design of robust, non-stoichiometric mixed metal oxides for oxygen electrocatalysis. In this research plan, we focus around the idea of tuning the metal ion composition and environment to create single atom centers with the utmost electrocatalytic activity. We hypothesized that tuning the cationic sites in nonstoichiometric mixed metal oxides will lead to single 4d/5d metal surface sites with optimal catalytic activity for low temperature oxygen reduction (ORR) and oxygen evolution (OER) at solid/liquid interfaces. We will focus on different crystal structures of these oxides including Ruddlesden-Popper (R-P) oxides, simple perovskites and pyrochlores due to their flexibility in accommodating different metal cation dopants, and the fact that they represent variations in the cationic arrangements in non-stoichiometric mixed metal oxide structures, which will lead to an understanding of how bulk crystal structure effects catalytic activity and stability of these systems.

08 HYDROGEN↗

DOE OSTI2021

NO 2 Interactions with MoO 3 and CuO at Atmospherically Relevant Pressures

NO x concentrations in some geographic regions are harmful to human health. Gas filters to trap NO x and other toxic chemicals contain metal oxides, including MoO 3 and CuO. These materials are also being investigated for NO x gas sensors. In a step to understand the fundamental adsorption mechanism in sensors and the effect on binding site availability in gas filters, ambient-pressure X-ray photoelectron spectroscopy (APXPS) was used to study the interaction of NO 2 with polycrystalline MoO 3 and CuO surfaces under pressures up to 0.01 Torr (14 parts per million volume (ppmv)). Density functional theory-based computational modeling was performed to reveal the mechanisms of NO 2 interactions with the MoO 3 (010) and CuO(111) surfaces to aid interpretation of the experimental results. With pressure dependence, NO 2 interacts with reduced Mo 5+ atoms generated by oxygen vacancies and abstracts hydrogen atoms from hydroxyl groups on MoO 3 without accumulating N-containing species on the surface; vacancy-induced electronic states in the band gap are also removed, hinting toward an increase in the resistivity of the material. N-containing species begin accumulating on the CuO surface at atmospherically relevant pressures of 140 ppbv. NO 2 only decomposes at oxygen vacancy sites of CuO. The nitrogen species leave the CuO surface upon evacuation, highlighting the importance of in situ surface characterization when studying gas sensing and adsorption mechanisms. Finally, these results imply that NO 2 removes hydroxyl and O vac binding sties on these materials when used in gas filtration and sensing applications. Furthermore, the results show the key role of O vac sites in the gas sensing mechanism of MoO 3 and highlight the potential of APXPS for further studies of gas sensors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

CONUS-wide Projected Flood Frequency and Uncertainty Estimates, Version 1.0

This dataset presents a large-ensemble of CONUS-wide projected flood frequency and uncertainty estimates across ~2.7 million NHDPlusV2 river reaches over the CONUS. The framework producing this dataset leverages a multi-model, uncertainty-aware modeling framework that allows evaluating shifts in flood frequences at the stream reach level across the CONUS. CONUS-wide ensemble streamflow projections generated from hydrologic simulations driven by downscaled and bias-corrected Coupled Model Intercomparison Project Phase 6 (CMIP6) outputs are used to derive these flood frequency and uncertainty estimates over the period 1980 - 2099. A spatially consistent regional L-moment algorithm is applied across clusters defined by the US Hydrologic Unit Code Subregions (HUC4s and HUC8s) and NHDPlusV2 stream orders to estimate flood frequencies. The dataset also includes at-site based flood estimates that allow for the comparison between local and regional approach-based estimates, assess projected changes, and characterize their uncertainties. For more reliable estimation of rare flood frequencies such as 500 and 1000-year return periods, super-ensemble based estimates are also included in the dataset. This dataset is derived to support the "Impact-Informed Dam Safety Risk Assessment for Securing Hydropower Assests" project for the US Department of Energy (DOE) Hydropower and Hydrokinetic Office (H2O). For further details, refer to Kao et al. (2022), Ghimire et al. (2023), Ghimire et al. (2025), and Hosking and Wallis (1997).

Ghimire, Ganesh [ORNL] (ORCID:0000000242843941)↗

DOE OSTI2020

Elemental characterization of crystalline silicotitanate following Hanford tank waste processing

To expedite vitrification of low activity waste at the Hanford Site, a Tank-Side Cesium Removal system is being evaluated. This method utilizes an inorganic ion exchange (IX) media, crystalline silicotitanate (CST), to remove 99.9% of the 137Cs from tank waste supernate. Laboratory scale testing of the ion exchange process has been conducted by Pacific Northwest National Laboratory to evaluate Cs removal with CST in supernates collected from Hanford tanks 241-AP-107 and 241-AW-102 under prototypic plant operating conditions. In an effort to understand the selectivity and partitioning of other analytes toward CST, specifically Resource Conservation and Recovery Act (RCRA) hazardous metals, selected +2 cations, and transuranic elements, a method for the complete dissolution of CST and Cs removal from the digestate was applied to the spent CST post-processing Hanford tank waste. The CST was shown to adsorb a relevant fraction of Ca, Cd, Pb, Sr, and potentially Fe by IX and/or other mechanisms. The spent CST also adsorbed actinides, including U, Pu, Np, and Am. This work discusses digestion of CST and removal of Cs from the digestate allowing effective analysis and provides insight as to what analytes may be competing for IX sites on the CST media.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Surface coverage dynamics for reversible dissociative adsorption on finite linear lattices

Dissociative adsorption onto a surface introduces dynamic correlations between neighboring sites not found in non-dissociative absorption. We study surface coverage dynamics where reversible dissociative adsorption of dimers occurs on a finite linear lattice. We derive analytic expressions for the equilibrium surface coverage as a function of the number of reactive sites, N, and the ratio of the adsorption and desorption rates. Using these results, we characterize the finite size effect on the equilibrium surface coverage. For comparable N’s, the finite size effect is significantly larger when N is even than when N is odd. Moreover, as N increases, the size effect decays more slowly in the even case than in the odd case. The finite-size effect becomes significant when adsorption and desorption rates are considerably different. These finite-size effects are related to the number of accessible configurations in a finite system where the odd-even dependence arises from the limited number of accessible configurations in the even case. We confirm our analytical results with kinetic Monte Carlo simulations. We also analyze the surface-diffusion case where adsorbed atoms can hop into neighboring sites. As expected, the odd-even dependence disappears because more configurations are accessible in the even case due to surface diffusion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Co 3 Ga 2 Ge 5 : Probing site mixing of the Ru 3 Sn 7 structure type with elements difficult to distinguish by diffraction

Co 3 Ga 2 Ge 5 was synthesized through arc-melting stoichiometric ratios of the elements, and a Ru 3 Sn 7 -type structure was confirmed by X-ray diffraction. Because Co 3 Ga 2 Ge 5 contains Ga and Ge, which have very similar X-ray and neutron scattering factors, any Ga/Ge crystallographic site preference cannot be determined with diffraction alone. The purpose of this study is to highlight the importance of using multiple techniques to characterize otherwise structurally ambiguous intermetallic compounds. Here, we utilize 71 Ga nuclear magnetic resonance spectroscopy and an analysis of the X-ray absorption fine structure to clarify the amount of Ga/Ge site mixing. Our combined use of X-ray diffraction and spectroscopy provides a comprehensive structural analysis of Ga site mixing across the Ge crystallographic sites, enhancing the understanding of the structure and properties of Co 3 Ga 2 Ge 5 .

36 MATERIALS SCIENCE↗

DOE OSTI2023

Performance Assessment Maintenance Plan for the Active Low-Level Burial Ground Trenches 31, 34, and 94 at the Hanford Site

This report documents the maintenance plan for the Hanford Site 200 West Area Active Low-Level Burial Ground Trenches 31 and 34 and 200 East Area Active Trench 94 performance assessment (PA). The PA maintenance plan is one of several supporting documents that are compendiums to the active trenches (Trenches 31, 34, and 94) PA as required in DOE O 435.1, Radioactive Waste Management . The PA is documented in DOE/RL-2021-26, Performance Assessment of Active Trenches in 200 East and West Low-Level Burial Grounds at the Hanford Site . This plan follows the requirements and outline specified in the applicable U.S. Department of Energy (DOE) standard used for developing documents supporting DOE-STD-5002-2017, Disposal Authorization Statement and Tank Closure Documentation . This maintenance plan summarizes the following major activities DOE plans to conduct to maintain the Trenches 31, 34, and 94 PA: Monitoring; Research and development; Planned reviews and analyses; Revisions of Trenches 31, 34, and 94 PA. The planned research and development activities relate to evaluating the key assumptions, including evaluating conceptual model assumptions and parameter value assumptions used in the PA. The planned research and development activities include those that are designed to track the release mechanisms for Category 1, Category 3, and uranium billet waste sources, as well as continued characterization and related modeling of the natural environment in the Central Plateau of the Hanford Site. In addition, the planned research and development activities include focused testing and evaluation of engineered and natural materials to reduce the uncertainty in the conceptual models and parameter values used in the PA. All key and secondary issues identified during the review of the PA by the Low-Level Waste Disposal Facility Federal Review Group have been resolved prior to finalization of the PA. There are no outstanding issues.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Stability of Floodplain Subsurface Microbial Communities Through Seasonal Hydrological and Geochemical Cycles

Riparian floodplains represent an interaction zone between the terrestrial subsurface and rivers, where regional groundwater flows, infiltration, and evapotranspiration drive mixing of water and import/export of nutrients and contaminants. These dynamics create seasonally transient redox conditions that drive biogeochemical transformations, which strongly modify groundwater quality. Microbial responses to changing hydrological conditions are perhaps the critical step connecting hydrology to geochemical transformations and groundwater quality, yet are not well understood. We aimed to address this knowledge gap by monitoring seasonal transitions at the U.S. Department of Energy legacy uranium ore processing site in Riverton, WY, through spring-summer-fall hydrological transitions. Our goal was to characterize the microbial community throughout the soil profile, down to the saturated aquifer, and observe its response to wet-dry transitions across a full season and compare to changes in geochemistry and hydrology. Next-generation sequencing was employed to identify biogeochemically-relevant microbial taxa based on the 16S rRNA gene; we found a broad diversity of microbial clades including taxa involved in sulfur and metal cycling, as well as nitrification. These data were paired with measurements of soil moisture, major nutrients and cations, and trace elements. Overall microbial community composition was dependent on soil depth or type, with seasonal effects only observed in the topsoil or subsurface aquifer. This finding indicates that microbial communities in the transiently-reduced center of the soil profile at the Riverton, WY site are remarkably stable, despite moisture and redox inversions. In addition, these communities likely impact the communities in surrounding soil horizons through export of metabolites and solutes as the water table rises and falls throughout the season.

16S rRNA↗

DOE OSTI2022

Atomically Dispersed CuN x Sites from Thermal Activation of Boron Imidazolate Cages for Electrocatalytic Methane Generation

Atomically dispersed metal sites (ADMSs) have been recognized as promising candidates for electrochemical conversion. Among a diverse range of molecular precursors for ADMS synthesis, framework materials are particularly interesting due to their high degree of tunability and control over the primary coordination sphere of the metal ions. In this work, we demonstrate that a copper boron imidazolate cage, BIF-29(Cu), is a convenient precursor for a competent catalyst with isolated Cu sites coordinated by N donors for carbon dioxide electroreduction (CO 2 RR). Although BIF-29(Cu) exhibited moderate methane selectivity over hydrogen evolution reaction (HER), the methane selectivity is significantly enhanced by 2 times (55% CH 4 at –1.25 V vs RHE) after mild thermal activation. Extensive characterization methods indicate the transformation of crystalline BIF-29(Cu) into an amorphous carbonaceous material comprising isolated CuN x sites. Moreover, in situ X-ray absorbance spectroscopy indicates stable CuN x sites that are reduced during CO 2 RR. This work encourages the discovery of single-site electrocatalytic systems through a rational selection of molecular precursor and calcination parameters for promoting product selectivity.

10 SYNTHETIC FUELS↗

DOE OSTI2023

Probing individual single atom electrocatalyst sites by advanced analytical scanning transmission electron microscopy

Single atom electrocatalysts (SAEs) are promising next-generation materials for promoting a variety of important reactions, such as the oxygen reduction, nitrogen reduction, and CO 2 reduction reactions. While bulk characterization techniques such as X-ray absorption spectroscopy and Mössbauer spectroscopy have significantly enhanced our understanding of these catalysts, direct probing of individual single metal atom sites at the atomic scale is necessary to understand local variations in the properties of these sites and accelerate design and synthesis of improved SAEs. Aberration-corrected scanning transmission electron microscopy (STEM) has become a powerful tool for providing this type of atomic-scale information about SAE metal sites. These sites are typically unstable under the electron beam, however, which, in combination with conventional acquisition methods and detectors, has limited the type and quantity of information obtainable by spectroscopic STEM techniques. Here, we map multiple individual SAE metal sites in a nitrogen-doped carbon containing atomically dispersed Fe and Re (FeReNC) at the atomic scale by direct electron detection electron energy-loss spectroscopy (EELS). Direct electron detection provides an improved signal-to-noise ratio over conventional scintillator-based detectors and enables detection and real space localization of weak signals. In addition, we demonstrate an automated method for identification of metal atom positions, placement of the probe on these sites, and simultaneous EELS and energy dispersive X-ray spectroscopic (EDS) signal acquisition. This simultaneous acquisition of EELS and EDS provides access to the composition and bonding of a wide range of SAE metal sites. In this study, focusing the probe directly on the metal sites also increases the relevant data acquisition rate by more than an order of magnitude over two-dimensional mapping, enabling improved statistical measurements of site properties. The versatility, sensitivity, and speed that these techniques provide enhances our ability to probe the local elemental and chemical environment of a large number of individual SAE metal site structures at the atomic scale, enabling an improved understanding of the variations in the local properties of these electrocatalysts to be gained. As a result, significantly increased information about individual metal sites will be available to future electrochemical studies through these techniques, accelerating the development of advanced SAEs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Spatial Study 2021: Sample-Based Surface Water Chemistry and Organic Matter Characterization across Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin. The dataset provides geochemistry and organic matter characterization data generated from samples collected during the same two-week period at 47 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. Related sensor data are published at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1892054. This data package was originally published September 2022. It was updated May 2023 (modified files) and November 2024 (new and modified files). See the change history section in the readme for more details. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved inorganic carbon (DIC), dissolved organic carbon (DOC; reported as non-purgeable organic carbon; NPOC), total nitrogen (TN), total suspended solids (TSS), ions, and benzene polycarboxylic acid (BPCA) concentration and stable isotope data; (5) averaged values from water chemistry data; (6) surface water sampling protocol; (7) sensor protocol (8) readme; (9) methods codes; (10) international generic-sample number (IGSN) mapping file; and (11) folder of high resolution characterization of organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). This folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formultitude (https://github.com/PNNL-Comp-Mass-Spec/Formultitude) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. We thank the United States Forest Service, Washington Department of Natural Resources, Washington Department of Fish and Wildlife, Washington State Parks, Confederated Tribes and Bands of the Yakama Nation, and Cowiche Canyon Conservancy for access to field locations where these samples were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

WHONDRS Surface Water and Sediment Non-Purgeable Organic Carbon and FTICR-MS across Glacial Features in Svalbard 2021 (v3)

This dataset supports a broader study examining land-atmosphere gas exchange associated with permafrost and glaciers in Svalbard. The dataset provides geochemistry and organic matter characterization data generated from surface water and sediment. Samples were collected from 8 spatially diverse sites across central Svalbard and also from a more comprehensive temporal and spatial study within one glacial catchment area throughout one summer melt season. Related data were collected and will be published separately in collaboration with Yde and Kleber.This data package was originally published in September 2022. It was updated in March 2023 (v2; new and modified files), and July 2025 (v3; modified files). See the change history section in the readme for details.For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved organic carbon (DOC; measure as non-purgeable organic carbon; NPOC); (5) surface water sampling protocol; (6) sediment extraction protocol; (7) readme; (8) methods codes; (9) international generic sample number (IGSN) mapping file; and (10) folder of high resolution characterization of organic matter via 7 and 12 Tesla (7T and 12T) Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) generated through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The FTICR folder contains two subfolders containing the 7T and 12T .xml data files and another subfolder containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Temporal Study 2021-2022: Sample-Based Surface Water Chemistry and Organic Matter Characterization across Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of temporal variability in sediment respiration rates in the Yakima River Basin. The dataset provides geochemistry and organic matter characterization data generated from samples collected at weekly or bi-weekly intervals at six sites across the Yakima River Basin in Washington, USA. Related sensor data will be published separately and can be used to link sediment respiration rates to biogeochemical processing rates. The data package was originally published in November 2022. It was updated in November 2023 (v2; modified files) and April 2025 (new and modified files). See the change history section in readme for more details. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved inorganic carbon (DIC), dissolved organic carbon (DOC; reported as non-purgeable organic carbon; NPOC), total nitrogen (TN), total suspended solids (TSS), and ions; (5) averaged values from water chemistry data; (6) surface water sampling protocol; (7) sensor protocol; (8) readme; (9) methods codes; (10) international generic sample number (IGSN) mapping file; and (11) folder of high resolution characterization of organic via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). This folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected our data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Single-Atom Metal Oxide Sites as Traps for Charge Separation in the Zirconium-Based Metal–Organic Framework NDC–NU-1000

Solvothermal deposition in metal–organic frameworks (MOFs) can be utilized to mount single-metal-atom catalytic species at chemically reactive sites on hexa-Zr(IV)-oxy(oxo,hydroxo,aqua) nodes in nanoscale crystallites of the MOF NDC-NU-1000 in a self-limiting fashion. Upon photoexcitation of the 1,3,6,8-tetrakis( p -benzoato)pyrene chromophores of the parent framework, charge transfer may occur between the chromophores and the installed heterometal sites. Extended X-ray absorption fine structure studies revealed the single-atom nature of the installed species. A combination of steady-state and ultrafast optical spectroscopy was utilized to uncover evidence of a charge-separated (CS) state arising in the metalated samples. The relevant dynamics were characterized with transient photoluminescence and femtosecond transient absorption spectroscopy. Here, we find that a titanium-oxy single atom site gives rise to the longest-lived CS species compared to cobalt and nickel in a similar arrangement. This study provides guidance in designing MOF-based catalytic systems for photocatalysis and solar-fuel production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

The Hyperthermophilic Restriction-Modification Systems of Thermococcus kodakarensis Protect Genome Integrity

Thermococcus kodakarensis (T. kodakarensis), a hyperthermophilic, genetically accessible model archaeon, encodes two putative restriction modification (R-M) defense systems, TkoI and TkoII. TkoI is encoded by TK1460 while TkoII is encoded by TK1158. Bioinformative analysis suggests both R-M enzymes are large, fused methyltransferase (MTase)-endonuclease polypeptides that contain both restriction endonuclease (REase) activity to degrade foreign invading DNA and MTase activity to methylate host genomic DNA at specific recognition sites. In this work, we demonsrate T. kodakarensis strains deleted for either or both R-M enzymes grow more slowly but display significantly increased competency compared to strains with intact R-M systems, suggesting that both TkoI and TkoII assist in maintenance of genomic integrity in vivo and likely protect against viral- or plasmid-based DNA transfers. Pacific Biosciences single molecule real-time (SMRT) sequencing of T. kodakarensis strains containing both, one or neither R-M systems permitted assignment of the recognition sites for TkoI and TkoII and demonstrated that both R-M enzymes are TypeIIL; TkoI and TkoII methylate the N 6 position of adenine on one strand of the recognition sequences GTGAAG and TTCAAG, respectively. Further in vitro biochemical characterization of the REase activities reveal TkoI and TkoII cleave the DNA backbone GTGAAG(N) 20 /(N) 18 and TTCAAG(N) 10 /(N) 8 , respectively, away from the recognition sequences, while in vitro characterization of the MTase activities reveal transfer of tritiated S-adenosyl methionine by TkoI and TkoII to their respective recognition sites. Together these results demonstrate TkoI and TkoII restriction systems are important for protecting T. kodakarensis genome integrity from invading foreign DNA.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Design Principles in Engineering of Multigrain Nanocatalysts via Multiscale Electronic Structure Characterization

Engineering grain boundary (GB) strain provides a promising pathway to tune the catalytic properties of nanocrystals. However, structural heterogeneity from random grain orientation and geometry has limited clear structure–property correlations. Here, we utilize a multigrain Co3O4/Mn3O4 core/shell nanocrystal platform as a model system to systematically investigate how geometric misfit strain at GBs serves as catalytically active sites for the oxygen reduction reaction. Through precise subnanometer-level control over grain morphology and by integrating multiscale electronic structure characterization, we identify the electronic structural signature of GB defects and establish a direct correlation between localized strain fields and modified electronic states. Strain modulation at GBs alters the eg orbital energy levels, with elongation along the z-axis combined with shear strain stabilizing the eg states, in contrast to the destabilization observed under pure shear strain. This stabilization mechanism enhances the electrocatalytic activity and selectivity of strained GBs compared with strain-relaxed grain surfaces. Furthermore, we reveal that GBs exhibit a radial strain gradient, producing a spatial energy shift that further modulates local electronic structures, as resolved through the classification of electron energy loss spectroscopy data. Together, these findings demonstrate that geometric misfit strain enables precise tuning of grain geometry and the resulting electronic structures, offering a robust strategy for engineering next-generation nanocatalysts.

Cho, Min Gee↗