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Genome-scale Design and Engineering of Non-model Yeast Organisms for Production of Biofuels and Bioproducts

The overall goal of this project was to develop genome-scale design and engineering tools for two non-model yeast organisms including Rhodotorula toruloides and Issatchenkia orientalis to produce high-levels of fatty acids-derived products and organic acids, respectively. The project was performed between 9/15/2017 and 9/14/2024 (the last two-years were no-cost extensions). The team consisted of Huimin Zhao (Lead PI) and Christopher Rao (Co-PI) from the University of Illinois at Urbana-Champaign (UIUC), Costas Maranas (Co-PI) from the Pennsylvania State University, Joshua Rabinowitz (Co-PI) and Martin Wuhr (Co-PI) from Princeton University, and Yasuo Yoshikuni (Co-PI) from the DOE Joint Genome Institute. The team has made great progress in both tool development and fundamental understanding of these two non-model yeasts. In total, there were 40 research publications (one of them is still under review) and one patent application as well as numerous oral presentations.

60 APPLIED LIFE SCIENCES↗

Affinity of LDR Organics to Cementitious Materials and Activated Carbon

The Hanford site stores approximately 56 million gallons of radioactive and hazardous waste in underground storage tanks. The current low-activity waste (LAW) vitrification facility does not have the capacity to immobilize all of the LAW. Therefore, cementitious waste forms are being evaluated as a cost-effective supplemental waste treatment, focusing on the solidification/immobilization of Land Disposal Restricted (LDR) organics, which is currently not recognized by the Environmental Protection Agency (EPA) as a standard treatment method (40 CFR 268.42). Previous efforts by the EPA and waste management agencies have highlighted the potential for cementitious materials to retain certain organic species through physical (encapsulation) and chemical (sorption) interactions.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

SPRUCE Warming Promotes the Use of Organic Matter as an Electron Acceptor in a Peatland: Supporting Data

These data are provided in support of the publication: Warming Promotes the Use of Organic Matter as an Electron Acceptor in a Peatland (Rush et al., 2021). Rush et al. (2021) reported on the effect of temperature on microbial organic matter reduction at the SPRUCE study site and S1 bog. Specifically, electron shuttling capacity (ESC), CH4 production, CO2 production, and acetate concentration were measured to explore both direct and indirect (through changes in soil quality and water-table level) effects of warming on microbial activity. Samples were collected in the summer of 2016 and 2017 depending on the experiment. This dataset contains five files in comma separated (*.csv) format. The SPRUCE Experiment Site is located in a Picea mariana [black spruce] Sphagnum spp. bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF). This ecosystem, which is located at the southern margin of the boreal forest, is considered especially vulnerable to climate change and anticipated to be near its tipping point.

54 ENVIRONMENTAL SCIENCES↗

Chloroform Fumigation Extraction for Microbial Biomass and Dissolved Organic Carbon from SPRUCE, Marcell Experimental Forest, Minnesota, 2021, 2022, and 2024

This data set provides the results for chloroform fumigation extraction (CFE) of peat samples collected from ambient and experimental plots in the Spruce and Peatland Responses Under Environmental Change (SPRUCE) Experiment site in June and August of 2021, June of 2022, and June, August, and October of 2024. The SPRUCE Experiment site is in the Marcell Experimental Forest in northern Minnesota, USA. The data set includes values for microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), dissolved organic carbon (DOC), dissolved nitrogen (DN), moisture content (MC, available for 2021 and 2022 only) and gravimetric water content (GWC) at 11 depth increments of two-meter peat cores taken from 12 sampling sites at SPRUCE (10 temperature treatment enclosures, 2 ambient temperature treatment enclosures). The sample analysis followed standard methods. The samples were analyzed using a Shimadzu Total Organic Carbon/Nitrogen (TOC/N) analyzer (TOC-V and TOC-L; 2021-2022) or an Elementar vario TOC Cube (2024), liquid catalytic oxidation combustion analyzers for total carbon and nitrogen analysis. This dataset contains two data files in comma separate (.csv) format. Additional metadata are provided: two data dictionaries and a file-level metadata file in comma separate (.csv) format and a user guide in PDF (*.pdf) format.

dissolved nitrogen↗

Culturing of “Unculturable” Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater

Recovery and cultivation of diverse environmentally-relevant microorganisms from the terrestrial subsurface remain a challenge despite recent advances in modern molecular technology. Here, we applied complex carbon (C) sources, i.e., sediment dissolved organic matter (DOM) and bacterial cell lysate, to enrich groundwater microbial communities for 30 days. As comparisons, we also included enrichments amended with simple C sources including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex C is far more effective in enriching diverse and distinct microorganisms from groundwater than simple C. Simple C enrichments yield significantly lower biodiversity, and are dominated by few phyla (e.g., Proteobacteria and Bacteroidetes ), while microcosms enriched with complex C demonstrate significantly higher biodiversity including phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia , Planctomycetes , and Armatimonadetes ). Subsequent isolation from complex C enrichments yielded 228 bacterial isolates representing five phyla, 17 orders, and 56 distinct species, including candidate novel, rarely cultivated, and undescribed organisms. Results from this study will substantially advance cultivation and isolation strategies for recovering diverse and novel subsurface microorganisms. Obtaining axenic representatives of “once-unculturable” microorganisms will enhance our understanding of microbial physiology and function in different biogeochemical niches of terrestrial subsurface ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

Improved Predictive Tools for Structural Properties of Metal–Organic Frameworks

The accurate determination of structural parameters is necessary to understand the electronic and magnetic properties of metal–organic frameworks (MOFs) and is a first step toward accurate calculations of electronic structure and function for separations and catalysis. Theoretical structural determination of metal-organic frameworks is particularly challenging because they involve ionic, covalent, and noncovalent interactions, which must be treated in a balanced fashion. Here, we apply a diverse group of local exchange-correlation functionals (PBE, PBEsol, PBE-D2, PBE-D3, vdW-DF2, SOGGA, MN15-L, revM06-L, SCAN, and revTPSS) to a broad test set of MOFs to seek the most accurate functionals to study various structural aspects of porous solids, in particular to study lattice constants, unit cell volume, two types of pore size characteristics, bond lengths, bond angles, and torsional angles). The recently developed meta functionals revM06-L and SCAN, without adding any molecular mechanics terms, are able to predict more accurate structures than previously recommended functionals, both those without molecular mechanics terms (PBE, PBEsol, vdW-DF2, and revTPSS) and those with them (PBE-D2 and PBE-D3). To provide a broader test, these two functionals are also tested for lattice constants and band gaps of unary, binary, and ternary semiconductors.

36 MATERIALS SCIENCE↗

Beyond Pristine Metal–Organic Frameworks: Preparation of Hollow MOFs and Their Composites for Catalysis, Sensing, and Adsorption Removal Applications

Metal–organic frameworks (MOFs) have been broadly applied to numerous domains with a substantial surface area, tunable pore size, and multiple unsaturated metal sites. Recently, hollow MOFs have greatly attracted the scientific community due to their internal cavities and gradient pore structures. Hollow MOFs have a higher tunability, faster mass-transfer rates, and more accessible active sites when compared to traditional, solid MOFs. Hollow MOFs are also considered to be candidates for some functional material carriers. For example, composite materials such as hollow MOFs and metal nanoparticles, metal oxides, and enzymes have been prepared. These composite materials integrate the characteristics of hollow MOFs with functional materials and are broadly used in many aspects. This review describes the preparation strategies of hollow MOFs and their composites as well as their applications in organic catalysis, electrochemical sensing, and adsorption separation. Finally, we hope that this review provides meaningful knowledge about hollow-MOF composites and their derivatives and offers many valuable references to develop hollow-MOF-based applied materials.

36 MATERIALS SCIENCE↗

Post-Wildfire Mobilization of Organic Carbon

Wildfires significantly alter watershed functions, particularly the mobilization of organic carbon (OC). This study investigated OC mobility and the physicochemical characteristics of wildfire-impacted soils and ashes from the northern California and Nevada fires (Dixie, Beckworth, Caldor). Organic carbon in wildfire-derived ashes (9.2–57.3 mg/g) generally exceeded levels in the background soils (4.3–24.4 mg/g), except at the Dixie fire sites. The mobile OC fraction varied from 0.0093 to 0.029 in ashes and 0.010 to 0.065 in soils, though no consistent trend was observed between the ashes and soils. Notably, the ash samples displayed lower OC mobility compared with the soils beneath them. A negative correlation was found between the mobile OC fraction and bulk OC content. Wildfire increased the total amount of mobile OC substantially by 5.2–574% compared to the background soils. Electron paramagnetic resonance (EPR) spectra confirmed the presence of environmentally persistent free radicals (EPFRs), which correlated with observed redox reactivity. Additionally, X-ray absorption near edge structure (XANES) and X-ray fluorescence (XRF) imaging revealed that Fe(II) oxidation in soils beneath the ashes may have enhanced the OC mobility, likely driven by pyrogenic carbon and free radicals. These findings enhance our understanding of post-wildfire OC mobilization and the impact of ash–soil physicochemical properties on watershed health.

organic carbon↗

Analysis of secondary organic aerosol simulation bias in the Community Earth System Model (CESM2.1)

Organic aerosol (OA) has been considered as one of the most important uncertainties in climate modeling due to the complexity in presenting its chemical production and depletion mechanisms. To better understand the capability of climate models and probe into the associated uncertainties in simulating OA, we evaluate the Community Earth System Model version 2.1 (CESM2.1) configured with the Community Atmosphere Model version 6 (CAM6) with comprehensive tropospheric and stratospheric chemistry representation (CAM6-Chem) through a long-term simulation (1988–2019) with observations collected from multiple datasets in the United States. We find that CESM generally reproduces the interannual variation and seasonal cycle of OA mass concentration at surface layer with a correlation of 0.40 compared to ground observations and systematically overestimates (69%) in summer and underestimates (-19%) in winter. Through a series of sensitivity simulations, we reveal that modeling bias is primarily related to the dominant fraction of monoterpene-formed secondary organic aerosol (SOA), and a strong positive correlation of 0.67 is found between monoterpene emission and modeling bias in the eastern US during summer. In terms of vertical profile, the model prominently underestimates OA and monoterpene concentrations by 37%–99% and 82%–99%, respectively, in the upper air (>500 m) as validated against aircraft observations. Our study suggests that the current volatility basis set (VBS) scheme applied in CESM might be parameterized with monoterpene SOA yields that are too high, which subsequently results in strong SOA production near the emission source area. We also find that the model has difficulty in reproducing the decreasing trend of surface OA in the southeastern US probably because of employing pure gas VBS to represent isoprene SOA which is in reality mainly formed through multiphase chemistry; thus, the influence of aerosol acidity and sulfate particle change on isoprene SOA formation has not been fully considered in the model. This study reveals the urgent need to improve the SOA modeling in climate models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thermodynamic Equilibrium in the Origin of Organic Matter

Theoretical and experimental support is presented for the hypothesis that organic compounds occurring in carbonaceous chondrites may have formed under equilibrium or near equilibrium conditions. The equilibrium distributions of organic compounds at temperature between 300 and 1000 K and pressures of 10(exp 16) to 50 atmospheres for the C-H-O system have been computed. At high temperatures and low pressures aromatic compounds may form even in the presence of excess hydrogen. Equilibrium concentrations of numerous compounds possible at 1000 K when N, S, and C1 are added to the system have also been determined. A limited equilibrium method is employed in which those few compounds which form with most difficulty are excluded from the computations. This approach is shown to be useful in the interpretation of certain experimental data. In preliminary experiments it has been found that gases, converted to the plasma state by high energy radio frequency discharge, yield product mixtures which are in qualitative agreement with those predicted.

CHEMICAL EQUILIBRIUM↗

Chemistry of the organic-rich hot core G327.3-0.6

We present gas-phase abundances of species found in the organic-rich hot core G327.3-0.6. The data were taken with the Swedish-ESO Submillimetre Telescope (SEST). The 1-3 mm spectrum of this source is dominated by emission features of nitrile species and saturated organics, with abundances greater than those found in many other hot cores, including Sgr B2 and OMC-1. Population diagram analysis indicates that many species (CH3CN, C2H3CN, C2H5CN, CH3OH, etc.) have hot components that originate in a compact (~2") region. Gas-phase chemical models cannot reproduce the high abundances of these molecules found in hot cores, and we suggest that they originate from processing and evaporation of icy grain mantle material. In addition, we report the first detection of vibrationally excited ethyl cyanide and the first detection of methyl mercaptan (CH3SH) outside the Galactic center.

NASA Discipline Exobiology↗

Chirality of Meteoritic Free and IOM-Derived Monocarboxylic Acids and Implications for Prebiotic Organic Synthesis

The origin of homochirality and its role in the development of life on Earth are among the most intriguing questions in science. It has been suggested that carbonaceous chondrites seeded primitive Earth with the initial organic compounds necessary for the origin of life. One of the strongest pieces of evidence supporting this theory is that certain amino acids in carbonaceous chondrites display a significant L-enantiomeric excess (ee), similar to those use by terrestrial life. Analyses of ee in meteoritic molecules other than amino acids would shed more light on the origins of homochirality. In this study we investigated the stereochemistry of two groups of compounds: (1) free monocarboxylic acids (MCAs) from CM2 meteorites LON 94101 and Murchison; and (2) the aliphatic side chains present in the insoluble organic matter (IOM) and extracted in the form of monocarboxylic acids (MCAs) from EET 87770 (CR2) and Orgueil (CI1). Contrary to the well-known ee observed for amino acids in meteorites, we found that meteoritic branched free and IOM-derived MCAs with 5-8 carbon atoms are essentially racemic. The racemic nature of these compounds is used to discuss the possible influence of ultraviolet circularly polarized light (UVCPL) and aqueous alterations on the parent body on chirality observed in in carbonaceous chondrites. 2014 Elsevier Ltd. All rights reserved.

monocarboxylic acids↗

Detection of Organics at Mars: How Wet Chemistry Onboard SAM Helps

For the first time in the history of space exploration, a mission of interest to astrobiology could be able to analyze refractory organic compounds in the soil of Mars. Wet chemistry experiment allow organic components to be altered in such a way that improves there detection either by releasing the compounds from sample matricies or by changing the chemical structure to be amenable to analytical conditions. The latter is particular important when polar compounds are present. Sample Analysis at Mars (SAM), on the Curiosity rover of the Mars Science Laboratory mission, has onboard two wet chemistry experiments: derivatization and thermochemolysis. Here we report on the nature of the MTBSTFA derivatization experiment on SAM, the detection of MTBSTFA in initial SAM results, and the implications of this detection.

astrobiology↗

Refractory Organics in Comet 67P Churyumov-Gerasimenko: Additional Evidence for Large-scale Mixing in the Primitive Solar Nebula?

The COSIMA instrument onboard the Rosetta spacecraft collected and analyzed samples of individual particles from the coma of Comet67P/ Churyumov-Gerasimenko. Initial results of the analysis of several particles have been presented elsewhere while analyses of the organic component of the dust particles has been shown to compare favor ably to laboratory spectra of IOM extracted from the Orguil and Murchison meteorites. Here we will compare the spectra of the same two particles to laboratory spectra of organic grain coatings produced via Surface Mediated Reactions of CO, H2 and N2 on amorphous iron silicate grains.

Refractory Organics↗

The Detection of Hot Cores and Complex Organic Molecules in the Large Magellanic Cloud

We report the first extragalactic detection of the complex organic molecules (COMs) dimethyl ether (CH3OCH3) and methyl formate (CH3OCHO) with the Atacama Large Millimeter/submillimeter Array (ALMA). These COMs, together with their parent species methanol (CH3OH), were detected toward two 1.3 mm continuum sources in the N 113 star-forming region in the low-metallicity Large Magellanic Cloud (LMC). Rotational temperatures (Trot approx. 130 K) and total column densities (Nrot 10 approx. 16 cm−2) have been calculated for each source based on multiple transitions of CH3OH. We present the ALMA molecular emission maps for COMs and measured abundances for all detected species. The physical and chemical properties of two sources with COMs detection, and the association with H2O and OH maser emission, indicate that they are hot cores. The fractional abundances of COMs scaled by a factor of 2.5 to account for the lower metallicity in the LMC are comparable to those found at the lower end of the range in Galactic hot cores. Our results have important implications for studies of organic chemistry at higher redshift.

complex organic molecules↗

Can Organic Haze and O2 Plumes Explain Patterns of Sulfur Mass-Independent Fractionation During the Archean?

The existence of mass-independently fractionated sulfur in Archean rocks is almost universally accepted as evidence for low atmospheric O2 and O3 concentrations at that time. But the detailed patterns of the values and of the ratios / and / remain to be explained, and the mechanism for producing the mass-independent fractionation remains controversial. Here, we explore the hypothesis that the relatively low values seen during the Mid-Archean, 2.7-3.5 Ga, were caused by the presence of organic haze produced from photolysis of methane. This haze helped shield SO2 from photolysis, while at the same time providing surfaces on which unfractionated short-chain sulfur species could condense. The evolution of oxygenic photosynthesis, and the concomitant disappearance of organic haze towards the end of the Archean allowed more negatively fractionated S4 and S8 to form, thereby generating large positive fractionations in other sulfur species, including sulfate and H2S. Reduction of this sulfate to H2S by bacteria, followed by incorporation of H2S into pyrite, produced the large positive values observed in the Neoarchean rock record, 2.5-2.7 Ga.

Great Oxidation Event↗