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Full ribosomal operon sequencing of anaerobic gut fungi (phylum Neocallimastigomycota ): insights on its markers and phylogenetic resolution

The phylogenetic affiliations of anaerobic gut fungi (Neocallimastigomycota) are typically evaluated using single-gene markers. However, this approach often fails to resolve relationships between closely related lineages. To address this issue and identify alternative markers, we created a curated database comprising the complete ribosomal operon sequences of 156 isolates, representing 20 of the 22 recognized genera and two new genus-level clades. Using long-read sequencing, we obtained ~9 kbp operon sequences and developed a robust analysis pipeline. Incorporating both coding genes and non-coding regions (excluding IGS1) improved phylogenetic resolution. This phylogenetic approach successfully resolved the Cyllamyces and Caecomyces clades (hard-to-distinguish genetically), as well as seven analysed Piromyces species. We also scanned the operon for markers that are suitable for short-read sequencing platforms, with the aim of enhancing biodiversity and phylogenetic studies. Notably, the ETS1 genetic region also enabled the distinction between these lineages, indicating its phylogenetic value within the ribosomal operon. The resulting database is a valuable resource for expanding and strengthening phylogenetic frameworks.

High-throughput sequencing

Green Era Anaerobic Digester

Green Era Educational NFP constructed and commissioned the Green Era Renewable Energy & Urban Farming Campus in Chicago’s Auburn Gresham neighborhood. The project transformed a long-vacant brownfield site into a commercial-scale anaerobic digestion facility that converts food waste into renewable natural gas and nutrient-rich material for agricultural use. The facility can process up to 80,000 wet tons of food waste annually and supports approximately 15 permanent jobs while advancing food waste diversion, renewable energy production, nutrient recovery and community revitalization.

03 NATURAL GAS

Eddy Covariance Theory: A Review

Eddy covariance (EC), the gold standard for measuring ecosystem scale gas and heat exchanges, has transformed our understanding of the breathing of the biosphere, and thus global change biology. Despite numerous methodological improvements and insights gained from the technique, the community faces persistent challenges that have been present since the first EC measurements. Here, we review the theoretical developments underpinning EC. We present theoretical developments in four important areas that have relevance to EC measurements of the net ecosystem exchanges (NEE) of gases and heat from a single tower: (i) measuring the total vertical flux density, (ii) flux attenuation, (iii) coordinate rotations, and (iv) energy balance closure. Persistent problems with EC measurements, such as the inability to close the energy budget, led us to identify two priorities for revisiting the theory underlying: (i) sensible heat flux calculations, and (ii) constraining the mean vertical wind velocity. We present a framework for improved calculation of sensible heat flux derived from first principles of fluid mechanics and thermodynamics that considers coupled heat and mass transfer so that conservation of both is obeyed. These refinements are motivated by the need for unbiased measurements of energy and mass transfer between the land surface and atmosphere for ecosystem research and to validate satellite observations and land surface models.

ecosystem fluxes

Calculating a minimum overlap period for successful intercalibration of soil moisture sensors

Abstract Long‐term in situ soil moisture monitoring inevitably requires sensors to be replaced. Ensuing discontinuities in the data record can be mitigated by intercalibration, however it is unclear how long the existing sensor needs to remain alongside the newly installed before there is enough overlapping data to generate a robust intercalibration. We used 154 pairs of established and newly installed sensors within the Marena, Oklahoma, In Situ Sensor Testbed to determine if there is a minimum overlap time that should be considered when planning upcoming replacements. Hourly observations of the existing sensor were linearly calibrated to those of the newly installed sensor with coefficients determined from overlap periods incremented by 30 days until a reference period of 2 years was reached. The resulting bias, root‐mean‐square error, and correlation coefficient for sensor pairs indicate that a minimum of 6 to 9 months of overlapping data are required to generate a successful intercalibration. Extending that to a full year before decommissioning the old sensor results in a stable intercalibration with higher confidence.

Agriculture

Metrology for femtosecond pulsed x-ray heating in diamond anvil cell experiments at the European XFEL: Revisiting the iron phase diagram up to 150 GPa

The development of pulsed intense x-ray sources, such as free electron laser, offers new avenues for high pressure experiments. Here, we study the feasibility and metrology of x-ray heating in diamond anvil cells at the European x-ray free electron laser. This method enables one to volumetrically heat the sample while inhibiting chemical migration and probing the crystallographic structure of the sample throughout the heating with a high repetition rate. We focus our study on iron, whose phase diagram is well established up to 100 GPa, to explore the possibilities and limitations of this technique. We volumetrically heat iron samples at starting pressures ranging from 10 to 138 GPa, using the x-ray beam pulsed at 4.5 MHz in a serial pump-and-probe experimental design. Experimental challenges arise from temperature gradients within the sample, changes in temperature at the 100 ns timescale, the difficulty of direct temperature estimates, the effect of thermal pressure, and the presence of metastable crystallites due to rapid cycles of heating and cooling. Hence, we develop a multi-crystal-like data processing method that allows us to account for sample heterogeneity in probed conditions. We then calibrate our measurements using known physical properties of iron under pressure. Thermal pressure in our experiments increases from 4% of the isochoric prediction at 10 GPa to 23% at 138 GPa, and we show that our data are in agreement with most previous observations of iron in this pressure range. The method can now be implemented at higher pressures and temperatures and on materials with unknown phase diagrams.

Materials science

Advancing technologies for lignin-based jet fuel production in aqueous phase

Integrating lignin into a cellulosic ethanol plant for the co-production of lignin-based jet fuel (LJF) in aqueous phase offers a significant opportunity to boost operational efficiency, economic viability, carbon conversion, and the overall sustainability of biofuel and chemical production. LJF is lignin-structure-based jet fuel blendstocks primarily composed of alkyl-substituted mono-, bi-, and tri-cyclohexanes. It exhibits high energy density, potential for low emissions, and favourable blend characteristics that comply with drop-in specifications. An overview of lignin feedstock, catalytic processes, LJF chemical compositions, fuel properties tests, and techno-economic analysis (TEA) and life cycle assessment (LCA) indicate that (1) the reactivity of lignin plays a crucial role in its structure transformation to LJF molecules; (2) catalytic processing of lignin to LJF can occur through a simultaneous depolymerization and hydrodeoxygenation process, bypassing the intermediate step of producing and upgrading lignin-derived oil; (3) LJF's uniqueness molecules making it more promising for high energy content and low emission jet fuel properties for next generation sustainable aviation fuel (SAF); and (4) TEA and LCA demonstrate that LJF is not only potentially cost-effective but also offers favourable carbon footprint compared to other SAFs. In conclusion, this review highlights the most recent advancements in LJF technology, along with the challenges and opportunities that lie ahead in fulfilling its potential.

09 BIOMASS FUELS

Weak, shallow, dry convection over Angola increases offshore stratocumulus cloud droplet number concentrations

Boundary-layer cloud interactions involving shortwave-absorbing aerosols remain one of the least understood aerosol influences on climate. Here, we find the highest stratocumulus cloud droplet number concentrations over the southeast Atlantic occur when agricultural fires coincide with synoptically-weakened surface warming over Angola, occurring June-early August. Dry convection fills a shallow continental boundary layer with smoke, and a nighttime (local solar time 2-9) land breeze transports the aerosol into the marine boundary layer. Offshore aerosol transport is strengthened by low-level easterlies from a continental pressure high southeast of Angola. Simultaneously, the South Atlantic subtropical high is weaker, allowing extensive dispersal of aerosol offshore into the boundary layer, obscuring cloud brightening from shipping. Meteorological co-variation at synoptic scales compensates for cloud brightening by the smoke. Outgoing shortwave radiation increases by 15–20% of the monthly mean in June and July when offshore droplet numbers are less but the stratocumulus deck is more developed.

54 ENVIRONMENTAL SCIENCES

Final Technical Report for DE-SC0022206

This project developed foundational genetic, genomic, and epigenetic tools for anaerobic fungi (Neocallimastigomycota), a group of microorganisms with exceptional natural abilities to deconstruct lignocellulosic biomass. Efficient biomass deconstruction remains a major barrier to economical production of renewable fuels, chemicals, and materials from agricultural and forestry residues. The project sought to enable mechanistic studies and future engineering of anaerobic fungi by improving genomic resources, establishing methods for gene expression, and investigating epigenetic regulation of biomass-degrading pathways. Major accomplishments included generation of the first chromosome-scale genome assemblies for multiple anaerobic fungal species, providing publicly available genomic resources that support both engineering and fundamental biological research. The project established the first reproducible system for heterologous gene expression in anaerobic fungi and identified genomic features and mobile genetic elements that may support future development of stable transformation technologies. In parallel, the project demonstrated direct conversion of untreated lignocellulosic biomass into fuels and specialty chemicals through a fungal-yeast bioprocess and identified anaerobic fungal enzymes with utility for metabolic engineering. The research also revealed that epigenetic regulation plays an important role in controlling fungal gene expression and enzyme production, identifying potential strategies for enhancing biomass degradation. Collectively, this work established anaerobic fungi as a tractable emerging platform for bioenergy and biomanufacturing research, generated valuable public resources, trained the next generation of researchers, and advanced DOE-BER goals related to predictive biology, sustainable bioprocessing, and the circular bioeconomy.

Solomon, Kevin [University of Delaware] (ORCID:000

Bioinspired Dry‐Steam Superinsulation Straw Foam

Abstract Cellulosic materials offer sustainable advantages for building energy conservation. However, their development has been hindered by reduced thermal performance, often caused by structural collapse during the transition from solution to solid. Inspired by natural goose down, a bio‐based, lightweight insulation foam derived from agricultural waste straw is presented. Through in situ synthesis, bio‐silica fibers with branched structures capable of supporting hollow silica microspheres are fabricated. After steam‐mediated processing, the resulting foam exhibit low density (95 mg cm − 3 ), high porosity (95.5%), low thermal conductivity (0.03 ± 0.003 W mK −1 ), and a cyclic compressive strength of 90 kPa at 50% strain. Owing to the synergistic microstructure formed by branched bio‐fibers and hollow silica spheres, the bio‐silica foam exhibit outstanding thermal insulation performance relative to other bio‐based foams prepared by ambient drying. A passivated insulation panel is further developed by incorporating this material as the core component, achieving a thermal conductivity of 0.0275 W mk −1 and flexural strength of 6.85 MPa. The panel demonstrated durability with stable thermal performance throughout a 60‐day outdoor test. Moreover, the bio‐silica foam shows a carbon footprint of 7.50 kgCO₂ kg −1 at 70.2 wt.% silica, highlighting its promise as a sustainable insulation solution for green buildings.

Chemistry

Biodegradable Biocomposite Development for Large Scale Additive Manufacturing

Oak Ridge National Laboratory (ORNL) worked with Mitsubishi Chemical America, Inc. to develop a highly biodegradable ~100% biobased feedstock for large format additive manufacturing (AM). Together, they developed an AM feedstock based on the biobased polyester, polybutylene succinate (PBS), that is typically used in agriculture and packaging projects. The motivation for this work was to leverage the high degradability of this polymer in AM to create a new avenue for end-of-life disposal of the product. A composite feedstock was developed from PBS, polylactic acid (PLA), and wood flour (WF). While WF improves printability, reduces feedstock cost, and can improve stiffness, it also often results in a loss in tensile strength which can inhibit/limit applications of the material. To recover the loss in tensile strength suffered by including large quantities, up to 30 wt.% WF in the composite, a chain extender was used to compatibilize the different composite constituents with each other. The feedstock was used to 3D-print a demonstration mold for precast concrete catch basins and was tested by casting 750 lbs of concrete. The mold survived the demonstration. Aerobic degradation testing of the composite feedstock showed that it was highly degradable, 40% biodegradation after 90 days, compared to other incumbent biobased feedstocks.

100% biobased feedstock for large format additive

Heterotrophic respiration by soil microbes in a changing climate

Soil microbes strongly influence the soil organic carbon (SOC) pool, which globally stores ~2,000 PgC. Specifically, the balance between microbial heterotrophic respiration (R H ), which degrades SOC, and plant–microbe interactions that stabilize SOC determines whether terrestrial ecosystems are a net source or sink of CO 2 to the atmosphere. Here, in this Review, we evaluate how climate change alters these competing processes. R H is approximately half of total soil respiration, at ~50 PgC yr −1 , with 70% occurring in topsoils. Warming accelerates microbial metabolism, with a 10 °C temperature increase estimated to raise R H by ~50%, an effect that is particularly strong in Arctic soils. Warming also reduces soil moisture, further modulating R H , which responds nonlinearly to soil moisture, being limited by saturation and desiccation and meeting a maximum at intermediate levels. Consequently, R H is highly sensitive to future precipitation changes and drought. However, soil management strategies could enhance SOC stocks and persistence under climate change. Bacterial and fungal inoculants can promote SOC production and stabilization, while deep-rooting plants increase SOC inputs to deeper layers that experience lower R H . Agricultural practices and biochar amendments can also enhance SOC and reduce R H . Expanding field trials across regions, climates and soil types would improve empirical understanding of these responses and support better representation of R H in predictive models, enabling more accurate assessments of climate impacts on SOC storage.

Jansson, Janet K. [Pacific Northwest National Labo

Renewable Energy and Efficiency Technologies in Scenarios of U.S. Decarbonization in Two Types of Models: Comparison of GCAM Modeling and Sector-Specific Modeling

Energy system projections from analytic models inform actions ranging from short-term and local decisions, such as technology and infrastructure deployment, to global and long-term negotiations and targets. Computational limits require the designers of these models to trade off between coverage and resolution. Some models, such as the Global Change Analysis Model (GCAM), represent all energy sources and uses but at a relatively coarse level of resolution. GCAM balances global supply and demand of all energy carriers by endogenously projecting prices for energy sources and costs of greenhouse gas mitigation while capturing interlinkages between the energy system, water, agriculture and land use, the economy, and the climate. This global model was used to frame the Long-Term Strategy released by the White House in 2021 and has been used to inform national and global economy-wide decarbonization discussions and strategy development for decades. Other models instead focus on a portion of the energy sector with greater detail and resolution. The Regional Energy Deployment System (ReEDS) electricity-sector model, for example, projects capacity expansion with an emphasis on integration of variable renewable energy into the grid of the future. The Transportation Energy and Mobility Pathway Options (TEMPO) transportation-sector model enables analysis of household choices in adoption, charging, and use of electric vehicles. The Scout buildings-sector model supports detailed consideration of the policies and markets that can accelerate the adoption of energy conservation measures in buildings. Such sector-specific models are instrumental in informing technology research, sectoral planning strategies, and sector-specific aspects of greenhouse gas (GHG) mitigation strategies in the United States. These global and sector-specific modeling approaches can complement each other. The global approach ensures consistent, endogenous energy pricing and resource allocation, which can substantially diverge from current conditions in transformative scenarios, while the sector-specific approach facilitates representation of granular details across spatial, temporal, technological, and market dimensions that enable exploration of particular interactions and trade-offs. This report presents the results of recent work to explore the differences and tradeoffs between these approaches by comparing GCAM with the sector-specific ReEDS, TEMPO, and Scout models. The report compares both model structures and results, and discusses their potential relevance and applications.

29 ENERGY PLANNING, POLICY, AND ECONOMY