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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species

Pseudomonas putida is a gram-negative bacterial species increasingly utilized in biotechnology due to its robust growth, ability to degrade aromatic compounds, solvent tolerance, and genetic tractability. In this study, we report a comprehensive multi-strain analysis of 164 P. putida strains based on the reconstruction of a pan-putida metabolic network and the formulation of strain-specific genome-scale metabolic models (GEMs). We performed whole-genome sequencing and hybrid assembly for 40 strains, contributing a ~8% increase to the available genomic data for P. putida . Furthermore, high-throughput phenotypic profiling using the Biolog phenotype microarray system for 24 strains on 190 unique carbon sources, along with 15 aromatic compounds not present on Biolog plates, yielded 4,920 unique strain-phenotype measurements. These data were leveraged to curate GEMs for 24 representative strains, including a refined model for strain KT2440, which comprised 1,480 genes and 2,191 metabolites, achieving a prediction accuracy of 91.2% in carbon utilization. Systematic comparison of genomes and GEMs revealed both conserved core pathways and significant allelic and functional divergence across strains, highlighting strain-specific variation in aromatic degradation. While pathways for protocatechuate and phenylacetate degradation were widely conserved, metabolic capabilities for compounds such as ferulate, phenol, and cresols varied markedly, suggesting adaptation to distinct ecological niches. Alleleome analysis of enzymes, such as PcaI and PcaJ, revealed distinct, functionally similar clades, indicating possible convergent evolution or horizontal gene transfer. These results provide computable resources and informative models for selecting P. putida strains with desired traits for biomanufacturing and bioremediation and offer insights into the evolution and phylogeny of the P. putida species.

aromatics utilization↗
DOE OSTI2026

Biochemical parallels between catabolic pathways for lignin-associated aromatic dimers

Lignin is one of the most common biopolymers on Earth. In nature, lignin is primarily deconstructed by fungi into mixtures of aromatic compounds that are then assimilated by bacteria and fungi. Industrially, lignin is primarily generated as a byproduct of pulp and paper production and burned for process heat. However, if the appropriate assimilatory pathways were identified, deconstructed lignin could be funneled into value-added products using engineered bacteria. Foundational work has described pathways for assimilation of diverse monomeric aromatic compounds such as protocatechuate, ferulate, and syringate, as well as select dimers including those with β-O-4 and 5-5 interunit linkages. Recent advances have elucidated additional pathways for dimer assimilation, including pathways for new substrates as well as parallel pathways for previously characterized substrates. Comparing these dimer assimilation pathways can illuminate the underlying biochemical logic of assimilation for lignin-associated aromatic dimers and provide opportunities for metabolic engineering to enhance lignin valorization.

Sphingomonas↗
DOE OSTI2025

Using a recirculating anaerobic dynamic membrane bioreactor to treat hydrothermal liquefaction aqueous by-product

Hydrothermal liquefaction (HTL) has the potential to improve resource recovery at water resource recovery facilities (WRRF), but the production of a high-strength aqueous by-product (HTL-aq) is hampering HTL implementation. The formation of biofilms in anaerobic digestion have been shown to be useful when degrading recalcitrant compounds present in HTL-aq due to the promotion of direct interspecies electron transfer (DIET) and increase in the microbial activity of syntrophic and methanogenic populations. The Recirculating Anaerobic Dynamic Membrane Bioreactor (RAnDMBr) was able to degrade 65% of the chemical oxygen demand (COD) at 1.5 ± 0.2 g COD LR −1 day −1 and 5.6 ± 2.3 days producing 0.19 ± 0.02 LCH4 gCOD fed −1 . However, adding a solution rich in nutrients on a daily basis was necessary. The system presented microbial populations able to degrade aromatic compounds (i.e., Anaerolinaceae) to perform DIET and syntrophy (i.e., Syntrophus) and methanogens (i.e., Methanobacterium and Methanosarcina) with the biofilm having a higher relative abundance of methanogens than the suspended biomass. Increasing the organic loading rate to 2 g COD LR −1 day −1 caused inhibition in the system by accumulation of volatile fatty acids, probably due to an increase in phenol, N-heterocyclic and aromatic compounds. Overall, this research shows that the RAnDMBr can be used to treat HTL-aq in WRRF without inhibition at OLRs of 1.5 ± 0.2 g COD LR −1 day −1 or lower, making HTL-aq treatment more feasible. Future research should focus co-digestion of HTL-aq with a co-substrate rich in nutrients and on fouling mitigation strategies that will allow to increase the recirculation ratio to promote advective substrate transport through the biofilm.

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

Microbial community dynamics and cycling of plutonium and iron in a seasonally stratified and radiologically contaminated pond

Plutonium (Pu) cycling and mobility in the environment can be impacted by the iron cycle and microbial community dynamics. We investigated the spatial and temporal changes of the microbiome in an iron (Fe)-rich, plutonium-contaminated, monomictic reservoir (Pond B, Savannah River Site, South Carolina, USA). The microbial community composition varied with depth during seasonal thermal stratification and was strongly correlated with redox. During stratification, Fe(II) oxidizers (e.g., Ferrovum, Rhodoferax, Chlorobium) were most abundant in the hypoxic/anoxic zones, while Fe(III) reducers (e.g., Geothrix, Geobacter) dominated the deep, anoxic zone. Sulfate reducers and methanogens were present in the anoxic layer, likely contributing to iron and plutonium cycling. Multinomial regression of predicted functions/pathways identified metabolisms highly associated with stratification (within the top 5%), including iron reduction, methanogenesis, C1 compound utilization, fermentation, and aromatic compound degradation. Two sediment cores collected at the Inlet and Outlet of the pond were dominated by putative fermenters and organic matter (OM) degraders. Overall, microbiome analyses revealed the potential for three microbial impacts on the plutonium and iron biogeochemical cycles: (1) plutonium bioaccumulation throughout the water column, (2) Pu–Fe-OM-aggregate formation by Fe(II) oxidizers under microaerophilic/aerobic conditions, and (3) Pu–Fe-OM-aggregate or sediment reductive dissolution and organic matter degradation in the deep, anoxic waters.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Novosphingobium aromaticivorans LigR coordinates transcription of genes involved in metabolism of multiple types of aromatics

Aromatic compounds are a ubiquitous and diverse family of chemicals with functions as biomolecules, natural products, industrial chemicals, and pollutants. Novosphingobium aromaticivorans DSM 12444 uses multiple inducible pathways to catabolize H-, G-, and S-type aromatics that contain zero, one, or two methoxy groups, respectively. Here, we obtain a systems-level view of the transcriptional control of its aromatic metabolic pathways. Several in vitro analyses found that a N. aromaticivorans homolog of the Sphingobium lignivorans SYK-6 transcription factor LigR bound genomic DNA upstream of genes involved in metabolism of multiple aromatic types. We found that a ΔLigR mutant had growth defects on all three types of aromatics as sole carbon sources. Transcriptomic analysis revealed that LigR was required to increase expression of gene products that function in metabolism of all three aromatic types. We also found that, in media containing both glucose and an aromatic carbon source, the ΔLigR mutant directed intermediates through alternative aromatic metabolic pathways. Protein-DNA binding assays showed that N. aromaticivorans LigR binds immediately upstream of promoters of genes involved in aromatic metabolism. We found that N. aromaticivorans LigR coordinates the expression of enzymes that function in the catabolism of H-, G-, and S-type aromatics, and that there are differences in the role of LigR in N. aromaticivorans and S. lignivorans. A comparative genomic analysis predicted that LigR homologs and the aromatic-metabolizing genes that it directly regulates are often co-localized in the genomes of Sphingomonadales, but often not found in this arrangement in many other known aromatic metabolizing bacteria.

Aromatic Compound Degradation↗
DOE OSTI2020

Elucidating the Chemical Pathways Responsible for the Sooting Tendency of 1 and 2-phenylethanol

Yield Sooting Index (YSI) measurements have shown that oxygenated aromatic compounds (OACs) tend to have lower YSI than aromatic hydrocarbon (AHC) compounds. For example, typical AHCs such as toluene and ethyl benzene have a YSI of 170 and 216, respectively, in contrast, OACs such as phenol and anisole have a YSI of 81 and 111, respectively. However, this trend is not always true as was observed for the structural isomers 1-phenylethanol (1PE, YSI=142) and 2-phenylethanol (2PE, YSI=207), where 2PE contains a YSI more representative of AHCs than OACs. We applied flow reactor experiments and density functional theory (DFT) calculations to examine how oxygen functionality present in 1PE and 2PE alters the reaction pathways leading to the observed difference in soot formation. It was determined that the proximity of the oxygen functional group to the aromatic ring determines whether the oxygen remains attached to the primary reacting species (for 1PE) or is eliminated early in the combustion sequence (for 2PE). For these alcohols, preservation of the oxygen in the molecule leads to further OACs, while loss of the oxygen leads to AHCs and benzyl radical. The direct pathways to AHCs and benzyl radical result in the higher YSI observed for 2PE.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Metabolism of Syringyl Lignin-Derived Compounds in Pseudomonas putida Enables Convergent Production of 2-Pyrone-4,6-Dicarboxylic Acid

Valorization of lignin, an abundant component of plant cell walls, is critical to enabling the lignocellulosic bioeconomy. Biological funneling using microbial biocatalysts has emerged as an attractive approach to convert complex mixtures of lignin depolymerization products to value-added compounds. Ideally, biocatalysts would convert aromatic compounds derived from the three canonical types of lignin: syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H). Pseudomonas putida KT2440 (hereafter KT2440) has been developed as a biocatalyst owing in part to its native catabolic capabilities but is not known to catabolize S-type lignin-derived compounds. Here, we demonstrate that syringate, a common S-type lignin-derived compound, is utilized by KT2440 only in the presence of another energy source or when vanAB was overexpressed, as syringate was found to be O-demethylated to gallate by VanAB, a two-component monooxygenase, and further catabolized via extradiol cleavage. Unexpectedly, the specificity (kcat/KM) of VanAB for syringate was within 25% that for vanillate and O-demethylation of both substrates was well-coupled to O2 consumption. However, the native KT2440 gallate-cleaving dioxygenase, GalA, was potently inactivated by 3-O-methylgallate. To engineer a biocatalyst to simultaneously convert S-, G-, and H-type monomers, we therefore employed VanAB from Pseudomonas sp. HR199, which has lower activity for 3MGA, and LigAB, an extradiol dioxygenase able to cleave protocatechuate and 3-O-methylgallate. This strain converted 93% of a mixture of lignin monomers to 2-pyrone-4,6-dicarboxylate, a promising bio-based chemical. Overall, this study elucidates a native pathway in KT2440 for catabolizing S-type lignin-derived compounds and demonstrates the potential of this robust chassis for lignin valorization.

2-pyrone-4,6-dicarboxylic acid↗
DOE OSTI2022

Biological Lignin Valorization

Given lignin's heterogeneity, catalytic depolymerization results in aromatic compound mixtures, and conversion of this complex substrate to a single product is challenging. To that end, the Biological Lignin Valorization (BLV) project is pursuing biological funneling, wherein aromatic catabolic microbes are engineered to convert a mixture of lignin-derived compounds to a single product. Namely, we employ Pseudomonas putida and pursue atom-efficient products, such as muconic acid, which can be further converted to direct replacements or used in performance-advantaged bioproducts. Overall, biological lignin conversion can make major contributions to reduce the minimum fuel selling price of the integrated biorefinery. Early industrial efforts in this area are also leading to value-added products, including in collaboration with the BLV project. Primary challenges associated with BLV efforts include accessing bio-available monomers from lignin (with the Lignin Utilization project), enabling commercial titers, rates, and yields of bioproducts from lignin-derived compounds, and overcoming substrate and product toxicity. To date, we have 1) demonstrated 49 g/L of muconate from aromatic compounds and 4 g/L of muconate from lignin, 2) improved the toxicity tolerance of P. putida to key aromatic substrates, 3) debottlenecked biological funneling for higher rates, and 4) engineered P. putida to convert S, G, and H-type lignin-derived compounds to a single product.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗
DOE OSTI2026

Ultranano Titania: Selectively Ridding Water of Persistent Organic Pollutants

Persistent organic pollutants, including the EPA's “dirty dozen”, are difficult to remove from water supplies due to their chemical stability. Here, we report a stable oxide photocatalyst, ultranano titania (d < 2 nm) doped with iron, Fe•TiUNP, that efficiently mineralizes multiple persistent pollutants including aromatic compounds plus common troublesome, difficult-to-oxidize intermediates such as formaldehyde and acetone, netting mineralization of persistent pollutants. Efficiency stems from a direct charge-transfer pathway. The key role of iron doping is to lower the reduction potential of the photogenerated electron so that it is insufficient to reduce water, thus eliminating competition from the hydrogen evolution reaction. The reduction potential of the localized electron is similarly insufficient to reduce quinone, enabling breaking aromaticity. Specific results for degrading acetone, phenol, benzoic acid, and 1,4-benzoquinone are reported.

alcohols↗
DOE OSTI2025

Whole genome sequence of the syntrophic benzoate-degrading bacterium, Syntrophus buswellii DSM 102354 T

The syntrophic obligate proton-reducing bacterium Syntrophus buswellii DSM 102354 T , isolated from anaerobic digester sludge, degrades benzoate and possibly hydrocinnamate (phenyl-3-propionate) when grown with a suitable hydrogenotrophic partner. The complete genome sequence data provide insight regarding aromatic compound degradation under thermodynamically limiting conditions when exogenous electron acceptors are absent.

Syntrophus↗
DOE OSTI2023

A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism

Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genome-scale model (GSM) of R. opacus PD630 metabolism based on its genomic sequence and associated data. The model includes 1773 genes, 3025 reactions, and 1956 metabolites, was developed in a reproducible manner using CarveMe, and was evaluated through Metabolic Model tests (MEMOTE). We combine the model with two Constraint-Based Reconstruction and Analysis (COBRA) methods that use transcriptomics data to predict growth rates and fluxes: E-Flux2 and SPOT (Simplified Pearson Correlation with Transcriptomic data). Growth rates are best predicted by E-Flux2. Flux profiles are more accurately predicted by E-Flux2 than flux balance analysis (FBA) and parsimonious FBA (pFBA), when compared to 44 central carbon fluxes measured by 13C-Metabolic Flux Analysis (13C-MFA). Under glucose-fed conditions, E-Flux2 presents an R2 value of 0.54, while predictions based on pFBA had an inferior R2 of 0.28. We attribute this improved performance to the extra activity information provided by the transcriptomics data. For phenol-fed metabolism, in which the substrate first enters the TCA cycle, E-Flux2’s flux predictions display a high R2 of 0.96 while pFBA showed an R2 of 0.93. We also show that glucose metabolism and phenol metabolism function with similar relative ATP maintenance costs. These findings demonstrate that iGR1773 can help the metabolic engineering community predict aromatic substrate utilization patterns and perform computational strain design.

Roell, Garrett W.↗
DOE OSTI2025

A distinct subpopulation of membrane vesicles in Pseudomonas putida is enriched in enzymes for lignin catabolism

Bacterial membrane vesicles (MVs) mediate diverse microbial processes and are emerging as powerful biomedical tools, but MV population heterogeneity remains an open question. Here, we separate, enumerate, and characterize two MV populations from the soil bacterium Pseudomonas putida during growth with or without lignin-derived carbon, a major carbon source from plant cells in the rhizosphere. Small MVs (MV-S, diameter ~100 nm) were produced from all cultures, whereas large MVs (MV-L, diameter ~300 nm) were observed during the late stationary phase of lignin cultivations. MV-S contained selectively packaged proteins with diverse physiological functions, whereas the MV-L proteome was smaller and largely enriched in outer membrane proteins. Interestingly, enzymes known to mediate the catabolism of lignin-derived aromatic compounds were enriched in MV-S. Overall, this study highlights the need for careful consideration of MV populations in microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Laboratory-Scale Coal-Derived Graphene Process (Final Report)

The Energy & Environmental Research Center (EERC) conducted a laboratory-scale coal-derived graphene (CDG) project focused on developing a technological process for making graphene from four U.S. domestic coal or coal wastes, including lignite from North Dakota, subbituminous coal from Wyoming, bituminous coal from Utah, and anthracite from Pennsylvania. The project was divided into two performance or budget periods (BPs), with BP1 comprising the up-front laboratory experiments to make graphene materials from coal beginning on May 1, 2020, to April 30, 2022. BP2 was conducted from May 1, 2022, to April 30, 2023, and was focused on analyzing the CDG process economic feasibility and the technical gaps for technological scale-up and commercialization. During this project, a few different coal-derived high-value products have been demonstrated, including graphite, graphene oxide (GO), reduced graphene oxide (rGO), and graphene quantum dots (GQDs). A new graphite microstructure was discovered and named “croissant graphite” because of the exterior morphological and textural resemblance to croissant food items sold in commercial groceries stores. The new graphite structure and the associated preparation from coal or coal waste feedstocks has been the subject of a U.S. patent application. The systematic experimental processes involving coal cleaning, upgrading, and conversion to high-value carbon products culminated into a developed upgraded coal-to-products (UCP) technology that is being pursued for potential fast-track commercialization, if funding is available. It is envisioned that commercialization of the UCP technology would increase consumption of U.S. domestic coals or coal wastes to make environmentally sustainable high-value products for the electronics industry, high-energy-storage applications, and clean energy technologies such as electric vehicle (EV) lithium-ion batteries (LIBs), for which graphite has become a critical mineral commodity. Croissant graphite microstructures, when observed by field emission scanning electron microscopy (FESEM), display wavy surface morphology and often grow from a base that is made of graphitized particles with honeycomb-like layers, which are believed to be graphene layers. While more studies are needed to fully ascertain the mechanisms of the croissant graphite microstructure formation, it is postulated that their growth may begin from curling of the graphene sheets into ribbon-like structures, and continuous growth and densification of the ribbon-like structures forms croissant microstructures. Additional studies are ongoing to evaluate the electrochemical performance of croissant graphite for LIB applications and to determine the experimental conditions necessary to tune on/off croissant formation so that it can be either optimized or suppressed depending on performance evaluation results. In addition to the discovery of croissant graphite, the graphitization process from the four coal ranks in general was successful. X-ray diffraction (XRD) analysis showed that the degree of graphitization (DoG) ranged from 12% to 80% in an early sample set, and further optimization on lignite coal produces a DoG of about 92%, which was spectacular to see as lignite is the lowest-rank coal. Thus, it is expected that the graphitization performance for higher-rank coals will be similar or better when optimized as well. The coal-derived graphite was used to make GO and rGO. Analytical characterization, e.g., by methods such as Raman spectroscopy, XRD, Fourier transform infrared (FTIR) spectroscopy and FESEM, showed that the sequence of converting the coal to graphite, exfoliating it to GO, and then chemically reducing the GO to rGO was successful. Although coal naturally contains aromatic compounds and some relatively small-sized condensed aromatic units, it does not contain graphene sheets. In the UCP process, the aromatic domains in the coals, particularly low-rank coals, are concentrated and condensed further into graphene sheets, which are ordered into a 3D stack during graphitization. The synthesized graphite is then unpacked by methods such as exfoliation to various graphene products. GQDs were synthesized from all four coal types, and their optical properties were demonstrated to be tunable by the coal precursor preprocessing treatments. In all four coal types, enhanced optical properties were observed for the produced GDQs with incremental improvements made to the coal precursors. GQDs produced from raw coal samples displayed lower ultraviolet–visible (UV–Vis) spectroscopy absorbance intensity compared to those obtained from cleaned and upgraded coal residues. The photoluminescence (PL) intensities also varied with pretreatment conditions and with the concentration of GQDs in aqueous solutions. GQDs obtained from anthracite show longer emission wavelengths and can be excited by visible light as opposed to GQDs derived from the other coal ranks. UV fluorescence 3D maps and spectra revealed that the emission wavelength at which the GQDs solutions display the highest intensity was slightly redshifted based on the coal precursor pretreatments. In low-rank coal (lignite and subbituminous) samples, two clusters were observed in the maps for GQDs, which may suggest that there are potentially two types of fluorophores in solution or two main size populations. The ability to tune the properties of GQDs based on processing methods can be exploited to make GQDs for various optical display or optoelectronics applications. The results also highlight the importance of removing coal-borne impurities to improve the quality of the coal precursor for preparation of graphene products. Coal and/or coal wastes preprocessing methods were developed and applied to clean and upgrade the coal precursors prior to graphitization and subsequent conversion to graphene products. The preprocessing methods involve high specific-gravity separations, mineral acid cleaning (no hydrofluoric acid), and subsequent upgrading by reducing the coal-borne heteroatom (nitrogen, sulfur, and oxygen) content using proprietary chemical agents. Analytical characterization revealed that the preprocessing steps were successful, with ash reductions that range from 38% to 80% and residual ash content that was below the 5 wt% initial target. Based on proximate and ultimate analysis, the heteroatom reduction reactions produced upgraded coal residues with the oxygen content reduced by 8% to 24%, with additional reductions in the nitrogen and sulfur contents. An initial assessment of the waste streams from the UCP process shows very small to negligible environmental impact due to CO 2 , NO x , and SO x because most process steps are performed under inert atmosphere with argon. Consequently, reactive oxygen environments that tend to create these species are avoided. The inorganic and potentially hazardous species are released into aqueous waste streams that are easy to handle for proper disposal. The liquid waste streams were found to contain low-level concentrations of rare-earth elements (REEs), which could be concentrated and recovered as value-added by-products. Additionally, the volatile and gaseous fractions from carbonization and heat treatment contain useful organic compounds that can also be recovered as potential valuable by-products. Thus, the UCP technology is considered an environmentally sustainable and promising emerging technology for making high-value products from coal and coal wastes, with potential additional value-added by-products. Analysis of potential markets for the coal-derived carbon products shows a strong demand in both niche market sectors and across a wide variety of other industrial sectors. Graphite is currently considered a critical mineral commodity that has a large and growing demand in the LIB industry for EV applications. Based on data from Fortune Business Insights (2022) and Marketwatch (2023) reports, the average global graphite market is projected to reach about 33 billion by 2028, growing at a compound annual growth rate (CAGR) of about 7%, with much of this growth expected to be in the LIB industry. GO and rGO have strong market potentials in various application areas, such as coatings for anticorrosion, anti-icing, and antimicrobial protection, thermal barriers, wear resistance, sensors, additive manufacturing such as 3D inks, and others. GQDs are the emerging key player in the bioimaging, photovoltaics, and light-emitting diodes (LEDs) applications, with the potential to replace traditional semiconductor quantum dots (SQDs), which are based on metallic systems that are more toxic and more expensive. Biomedical applications of GQDs are becoming more attractive because of low to no toxicity and extremely low cost compared to SQDs. The major challenges for scale-up and commercialization of coal-derived carbon products such as graphene vary from the inherent attributes of graphene itself to reluctance to accept graphene in new manufacturing processes because of the uncertainty of the unknown. The 2D nature of graphene materials with a thickness of one atom presents significant challenges to proper handling/processing, and process scale-up becomes difficult because it requires high-end, expensive equipment, even for routine handling and analysis for quality assurance and control. Pristine graphene can also be extremely difficult to work into other matrices, thus hindering downstream processibility, especially at large scale. Currently, the cost of graphene and graphene products is still high and presents an economic risk that tends to slow down investment in scaling up emerging technologies. The lack of a standard for graphene materials for quality assurance and quality control poses a great challenge not only for the markets but also for commercialization efforts. A first-look economic feasibility analysis of the UCP technology provided valuable information that suggests the UCP process would be feasible, especially when it is scaled to a pilot scale and could be more competitive at the full scale. Graphitization was found to be the most energy-consuming and most capital-intensive step in the overall process. In small laboratory- and bench-scale experiments, labor is a significant contributor to the total process costs. Although these energy, capital, and labor constraints contribute to a higher selling price for the product, a preliminary economic model suggests that the process would be feasible at large scale when the process is fully integrated, optimized, and automated.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

Topography and canopy cover influence soil organic carbon composition and distribution across a forested hillslope in the discontinuous permafrost zone

Abstract Topography and canopy cover influence ground temperature in warming permafrost landscapes, yet soil temperature heterogeneity introduced by mesotopographic slope positions, microtopographic differences in vegetation cover, and the subsequent impact of contrasting temperature conditions on soil organic carbon (SOC) dynamics are understudied. Buffering of permafrost‐affected soils against warming air temperatures in boreal forests can reflect surface soil characteristics (e.g., thickness of organic material) as well as the degree and type of canopy cover (e.g., open cover vs. closed cover). Both landscape and soil properties interact to determine meso‐ and microscale heterogeneity of ground warming. We sampled a hillslope catena transect in a discontinuous permafrost zone near Fairbanks, Alaska, to test the small‐scale (1 to 3 m) impacts of slope position and cover type on soil organic matter composition. Mineral active layer samples were collected from backslope, low backslope, and footslope positions at depths spanning 19 to 60 cm. We examined soil mineralogical composition, soil moisture, total carbon and nitrogen content, and organic mat thickness in conjunction with an assessment of SOC composition using Fourier‐transform ion cyclotron resonance mass spectrometry (FT‐ICR‐MS). Soils in the footslope position had a higher relative contribution of lignin‐like compounds, whereas backslope soils had more aliphatic and condensed aromatic compounds as determined using FT‐ICR‐MS. The effect of open versus closed tree canopy cover varied with the slope position. On the backslope, we found higher oxidation of molecules under open cover than closed cover, indicating an effect of warmer soil temperature on decomposition. Little to no effect of the canopy was observed in soils at the footslope position, which we attributed, in part, to the strong impact of soil moisture content in SOC dynamics in the water‐gathering footslope position. The thin organic mat under open cover on the backslope position may have contributed to differences in soil temperature and thus SOC oxidation under open and closed canopies. Here, the thinner organic mat did not appear to buffer the underlying soil against warm season air temperatures and thus increased SOC decomposition as indicated by the higher oxidation of SOC molecules and a lower contribution of simple molecules under open cover than the closed canopy sites. Our findings suggest that the role of canopy cover in SOC dynamics varies as a function of landscape position and soil properties, namely, organic mat thickness and soil moisture. Condition‐specific heterogeneity of SOC composition under open and closed canopy cover highlights the protective effect of canopy cover for soils on backslope positions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Topography and canopy cover influence soil organic carbon composition and distribution across a forested hillslope in the discontinuous permafrost zone

This dataset contains data used for the paper "Topography and canopy cover influence soil organic carbon composition and distribution across a forested hillslope in the discontinuous permafrost zone". The Related References field will be updated with a full citation when available. Topography and canopy cover influence ground temperature in warming permafrost landscapes, yet soil temperature heterogeneity introduced by meso-topographic slope positions, microtopographic differences in vegetation cover, and the subsequent impact of contrasting temperature conditions to soil organic carbon (SOC) dynamics are understudied. Buffering of permafrost-affected soils against warming air temperatures in boreal forests can reflect surface soil characteristics (e.g., thickness of organic material) as well as the degree and type of canopy cover (e.g., open cover vs closed cover). Both landscape and soil properties interact to determine meso- and micro-scale heterogeneity of ground warming. We sampled a hillslope catena transect in a discontinuous permafrost zone near Fairbanks, Alaska to test the small-scale (1 to 3 meter) impacts of slope position and cover type on soil organic matter composition. Mineral active layer samples were collected from backslope, low backslope, and footslope positions at depths spanning 19 to 60 cm. We examined soil mineralogical composition, soil moisture, total carbon and nitrogen content, and organic mat thickness in conjunction with an assessment of SOC composition using Fourier-transform ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS). Soils in the footslope position had a higher relative contribution of lignin-like compounds while backslope soils had more aliphatic and condensed aromatic compounds as determined by FT-ICR-MS. The effect of open versus closed tree canopy cover varied with slope position. On the backslope, we found higher oxidation of molecules under open cover compared with closed cover, indicating an effect of warmer soil temperature on decomposition. Little to no effect of canopy was observed for soils at the footslope position, which we attributed, in part, to the strong impact of soil moisture content in SOC dynamics in the water-gathering footslope position. The thin organic mat under open cover on the backslope position may have contributed to differences in soil temperature and thus SOC oxidation under open and closed canopy. Here, the thinner organic mat did not appear to buffer the underlying soil against warm season air temperatures and thus increased SOC decomposition as indicated by higher oxidation of SOC molecules and a lower contribution of simple molecules under open cover compared with the closed canopy sites. Our findings suggest that the role of canopy cover in SOC dynamics varies as a function of landscape position and soil properties, namely organic mat thickness and soil moisture. Condition-specific heterogeneity of SOC composition under open and closed canopy cover highlights the protective effect of canopy cover for soils on backslope positions. This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv format, which can be accessed and processed using MS Excel or R. This archive can also be accessed on GitHub at https://github.com/Erin-Rooney/Y1_fairbanks (DOI: 10.5281/zenodo.8071247).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Closing the loop on plastics: Biological and hybrid routes for converting plastic waste to polyhydroxyalkanoates

Polyhydroxyalkanoate (PHA) production from plastic-derived substrates offers a promising route to mitigate plastic pollution while reducing dependence on conventional PHA feedstocks. Plastic waste represents an abundant carbon source for microbial fermentation, but efficient conversion remains limited by incomplete deconstruction, inhibitory intermediates, low carbon recovery, and challenges in process integration. Plastic-derived streams contain diverse compounds, including fatty acids, hydrocarbons, fatty alcohols, aldehydes, esters, and aromatic compounds generated during depolymerization. These intermediates can be metabolized by selected microorganisms, particularly Pseudomonas species with versatile fatty-acid and hydrocarbon pathways, as well as Cupriavidus necator and mixed microbial cultures. Unlike reviews that address plastic upcycling or PHA biosynthesis separately, this review focuses on the deconstruction–fermentation interface that governs plastic-to-PHA conversion. It consolidates current progress in plastic deconstruction, substrate conditioning, microbial metabolism, fermentation control, polymer recovery, and techno-economic and life-cycle considerations. Here, by emphasizing substrate composition, biological compatibility, plastic‑carbon recovery, and final polymer quality, the review identifies priorities for scalable and environmentally sustainable PHA production from plastic-derived substrates.

42 ENGINEERING↗
DOE OSTI2021

Polycarboxylated compounds and compositions containing same

Methods of selectively modifying lignin, polycarboxylated products thereof, and methods of deriving aromatic compounds therefrom. The methods comprise electrochemically oxidizing lignin using stable nitroxyl radicals to selectively oxidize primary hydroxyls on β-O-4 phenylpropanoid units to corresponding carboxylic acids while leaving the secondary hydroxyls unchanged. The oxidation results in polycarboxylated lignin in the form of a polymeric β-hydroxy acid. The polymeric β-hydroxy acid has a high loading of carboxylic acid and can be isolated in acid form, deprotonated, and/or converted to a salt. The β-hydroxy acid, anion, or salt can also be subjected to acidolysis to generate various aromatic monomers or oligomers. The initial oxidation of lignin to the polycarboxylated form renders the lignin more susceptible to acidolysis and thereby enhances the yield of aromatic monomers and oligomers obtained through acidolysis.

Stahl, Shannon S.↗