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At least 19 records

From chromatin to crop: epigenetic innovations in bioenergy systems

Energy crops encompass a diverse array of plant species cultivated primarily as a source of biomass for energy generation and biofuel production. As such, they play a pivotal role in the transition to sustainable energy systems. However, their productivity is often limited by environmental stresses, nutrient availability, and the need for optimized yield. While traditional breeding and genetic engineering have driven improvements, challenges such as narrow genetic diversity, long development cycles, trait instability, and unexpected gene interactions remain. Epigenetics offers a largely untapped opportunity to overcome these constraints by regulating gene expression through mechanisms that are dynamic, finely tuned, and responsive to environmental and developmental cues. Epigenetic modifications including DNA methylation, histone post-translational changes, and small non-coding RNAs influence nearly all aspects of plant development and physiology, including traits central to bioenergy crops. While these mechanisms are well characterized in model species such as Arabidopsis thaliana, they remain underexplored in many purpose-grown energy crops. This review summarizes the current state of knowledge of epigenetic regulation in bioenergy species, explores how these mechanisms can be leveraged to enhance crop resilience and productivity, and identifies gaps in our understanding. By characterizing epigenetic mechanisms and harnessing epigenetic variation, we can expand the toolkit for developing resilient, high-yielding bioenergy crops to meet future environmental and energy demands.

09 BIOMASS FUELS

Accumulation of Soil Microbial Necromass Controlled by Microbe–Mineral Interactions

Soil organic matter (SOM) is a key reservoir for global carbon (C), supporting soil fertility and influencing greenhouse gas emissions. Microbial residues, composed of dead cells and cellular fragments, are major contributors to SOM formation. Yet, mechanisms by which minerals enhance the accumulation of microbial residues remain poorly understood. Here, we used 13 C-labeled glucose in a year-long incubation to trace microbial residue in sandy and silty soils. Across both soils, approximately 89% of retained microbial 13 C was recovered in the fine (<53 μm) mineral-associated organic matter (MAOM) pool. Within this pool, the light MAOM fraction, enriched in poorly crystalline Fe minerals, held 4.3 times more 13 C than the heavy, phyllosilicate-dominated MAOM fraction, despite accounting for only 17.2% of the total MAOM mass and 12.3% of the total soil mass. Along with 13 C enrichment, the light MAOM fraction showed greater abundance of N-containing groups, e.g., (amides and amino groups), indicative of microbial-derived compounds like proteins and amino sugars. Fe oxides in light MAOM from both soils were spatially dispersed. Microbial residue accumulation was greater in finer-textured silty soil. These findings demonstrate that mineral composition and texture jointly regulate microbial necromass accrual, highlighting light MAOM as a key pool for enhancing soil C storage.

13C isotope labeling

Agricultural Management Legacy Effects on Switchgrass Growth and Soil Carbon Gains

Switchgrass ( Panicum virgatum L.) is a native North American grass currently considered a high-potential bioenergy feedstock crop. However, previous reports questioned its effectiveness in generating soil organic carbon (SOC) gains, with resultant uncertainty regarding the monoculture switchgrass's impact on the environmental sustainability of bioenergy agriculture. We hypothesize that the inconsistencies in past SOC accrual results might be due, in part, to differences in prior land management among the systems subsequently planted to switchgrass. To test this hypothesis, we measured SOC and other soil properties, root biomass, and switchgrass growth in an experimental site with a 30-year history of contrasting tillage and N-fertilization treatments, 7 years after switchgrass establishment. We determined switchgrass' monthly gross primary production (GPP) for six consecutive years and conducted deep soil sampling. Nitrogen fertilization expectedly stimulated switchgrass growth; however, a tendency for better plant growth was also observed under unfertilized settings in the former no-till soil. In topsoil, SOC significantly increased from 2007 to 2023 in fertilized treatments of both tillage histories, with the greatest increase observed in fertilized no-till. Fertilized no-till also had the highest particulate organic matter content in the topsoil, with no differences among the treatments observed in deeper soil layers. However, regardless of fertilization, the tillage history had a strong effect on stratification with depth of SOC, total N, and microbial biomass C. Results suggested that historic and ongoing N fertilization had a substantial impact on switchgrass growth and soil characteristics, while tillage legacy had a much weaker, but still discernible, effect.

bioenergy crop production system

A 13‐Year Record Indicates Differences in the Duration and Depth of Soil Carbon Accrual Among Potential Bioenergy Crops

Six years after replacing a maize/soybean cropping system, perennial grasses miscanthus (Miscanthus × giganteus) and switchgrass (Panicum virgatum), and a 28-species restored prairie increased particulate organic carbon in surface soils without increasing soil organic carbon (SOC). To resolve potential changes in the quantity and distribution of SOC, soils were resampled after seven to thirteen years to measure bulk density, carbon (C) content, and stable C isotopes to a depth of 1 m. SOC stocks increased between 1.75 and 2.5 Mg ha −1 year −1 in all perennial crops between 2008 and 2016 (nine growing seasons). Despite relatively low litter inputs and belowground biomass, the highest rate of SOC accrual was in restored prairie (2.5 Mg ha −1 year −1 ), followed by miscanthus (2.0 Mg ha −1 year −1 ) and switchgrass (1.75 Mg ha −1 year −1 ). The change in SOC in maize/soybean was not significant. After 2016, total SOC decreased in maize/soybean and miscanthus, resulting in slower overall rates of SOC accumulation over the full sampling period for miscanthus (0.8 Mg ha −1 year −1 ). The rate of SOC accumulation was greatest below 50 cm depth for restored prairie and switchgrass but in the top 10 cm for miscanthus. Stable isotope analysis showed 13 C enrichment in all depths of switchgrass soils, an indication of new organic C accumulation, but mixed results in all other crops. Planting perennial crops on land formerly in an annual maize/soybean cropping system can slow or reverse soil carbon losses, with the greatest increases in SOC from species-rich prairie.

agriculture

Opportunities for bioenergy crops to support transitions from irrigated agriculture and conserve the U.S. High Plains Aquifer

This study investigates potential economic and groundwater driven transitions from irrigated maize production—the dominant irrigated cropping system in the High Plains Aquifer (HPA) region—to alternative crops such as sorghum and switchgrass, two common bioenergy feedstocks. Unsustainable groundwater extraction in the U.S. High Plains presents critical challenges including reduced irrigation capacities, diminished crop yields, lower land values, and escalating energy costs. Using a spatially explicit optimization framework combined with comprehensive economic and hydrogeological data, we evaluate optimal land-use strategies and irrigation system investments over a 30-year planning period. Results indicate significant regional variability in the future economic viability of irrigated agriculture, driven by differences in aquifer recharge rates, groundwater availability, and market conditions. Nebraska and parts of northern Texas can sustain irrigated maize profitability due to relatively favorable groundwater conditions and lower land rents, respectively. In contrast, many portions of Kansas and southern Texas are more likely to transition to dryland agriculture within two decades. Colorado and New Mexico show potential for significant adoption of switchgrass production as an alternative biomass-based energy crop. Overall, over the 30-year horizon, our model implies that approximately 23% of currently irrigated maize area across the HPA region may transition to dryland farming under business-as-usual conditions. This transition is complemented by a threefold increase in non-irrigated sorghum production, from 0.20 to 0.77 Mt yr−1, indicating that groundwater-driven shifts in agricultural production may support a larger regional base for bioenergy feedstocks. The study also reveals opportunities for producers to optimize economic returns and biomass production potential.

60 APPLIED LIFE SCIENCES

Contrasting Carbon–Water–Energy Dynamics in Perennial and Annual Bioenergy Agroecosystems Using Eddy Covariance and Interpretable Machine Learning

Understanding how agroecosystems respond to environmental variability is fundamental to predicting productivity and sustainability under a changing climate. We analyzed 55 site-years of high-frequency eddy covariance observations from five agroecosystems—two perennial grasses (miscanthus and switchgrass), two annual rotation systems (maize–soybean and sorghum–soybean), and a restored native prairie—to examine ecosystem-scale carbon, water, and energy fluxes. Using an interpretable machine-learning framework with regression tree ensembles, Shapley Additive Explanations, and Accumulated Local Effects, we quantified how environmental and temporal factors regulate gross primary productivity (GPP), evapotranspiration (ET), water-use efficiency, and the Bowen ratio. Perennials exhibited stronger physiological buffering and maintained fluxes across a broader range of temperature and moisture conditions, reflecting deeper rooting and persistent canopy cover. Annuals, in contrast, showed greater short-term variability and stronger coupling to atmospheric demand, with GPP and ET declining rapidly under low humidity or soil moisture. Differences in temperature sensitivity of Bowen ratio further revealed that perennials sustained proportionally greater sensible heat flux under cool conditions, whereas annuals exhibited constrained energy exchange when evaporative demand was low. Together, these results demonstrate that crop life cycle and canopy structure are fundamental determinants of ecosystem-scale carbon–water–energy coupling. By integrating long-term flux observations with interpretable machine learning, this study identifies the environmental drivers that shape agroecosystem function and highlights how conversion from annual to perennial feedstocks can enhance climatic resilience and alter land–atmosphere energy feedbacks. These findings provide a data-driven basis for improving crop and Earth-system models and for guiding bioenergy landscape design under future climate scenarios.

Accumulated Local Effects

Integrated Modeling Driven Evaluation of Opportunities for Climate‐Resilient Perennial Biomass Crop Plantings in Flood‐Prone Agricultural Landscapes

Adapting to future climate change in flood-prone landscapes will require climate-resilient agricultural systems. Planting perennial crops, like switchgrass and willow, along river corridors can mitigate future flooding while supporting bioenergy markets. We developed an integrated assessment linking climate, hydrologic, and inundation model results to assess future flood risk to river-adjacent agricultural lands in the Mid-Atlantic Region (MAR) and explore this opportunity. We produced ensemble streamflow projections for every MAR stream using a hydrologic model driven by a suite of downscaled and bias-corrected Coupled Model Intercomparison Project Phase 6 climate projections. We then conducted high-resolution inundation mapping based on projected flood frequencies for baseline and future periods. Results show that in the near-term future, at least two-thirds of the streams will experience 100-year floods more severe than the baseline 200-year floods. Riparian zones are projected to face a median rise of inundation by 9.5%–24.1%. Results show that there is an opportunity to mitigate flooding in over half of MAR's counties with the quantities of switchgrass and willow plantings anticipated for mature bioenergy markets, even under the most extreme (200-year) flood events. Our integrated modeling framework can guide similar regions to evaluate opportunities for flood-resilient agricultural systems under climate change.

60 APPLIED LIFE SCIENCES

Bioenergy Cropping Reduces the Spatiotemporal Scaling of Soil Bacterial Biodiversity

Widespread bioenergy cropping can transform landscapes, strongly affecting biodiversity. However, the impact of bioenergy cropping on the spatiotemporal scaling of soil biodiversity remains virtually unknown, despite its profound implications for the functioning of the ecological community. Here, we investigated how bioenergy cropping influenced the spatiotemporal scaling of soil bacterial biodiversity in marginal soils (sandy loam and clay loam soils) in Oklahoma, USA. We detected strong, significant species-time-area relationships (STARs) and phylogenetic-time-area relationships (PTARs) in bacterial communities and their lineages, suggesting that STARs and PTARs exist in microbial ecology within the studied system. Also, spatiotemporal scaling rates (the slopes of STAR and PTAR models) varied substantially among bacterial lineages and were positively correlated with their 16S rRNA gene copy numbers, a genomic trait indicative of microbial growth potentials. Strikingly, bioenergy cropping significantly reduced spatiotemporal scaling rates by 6.8%-14.1%, with a more pronounced reduction observed in sandy loam soils, where those rates were significantly lower than in clay loam soils. The heterogeneity of soil phosphorus and carbon resulted in variations in bacterial spatiotemporal scaling rates. Collectively, our findings suggest that bioenergy cropping may alleviate rapid shifts in soil biodiversity across space and time, thereby stabilizing soil biodiversity and supporting its role as part of sustainable land management and climate mitigation strategies.

bacterial diversity

Available land for cellulosic biofuel production: a supply chain centered comparison

The land that is potentially available to produce dedicated cellulosic bioenergy crops, often referred to as 'marginal' land, depends heavily on the underlying assumptions used to classify and identify it. In this study we compare three definitions and types of marginal land to identify the interactions between the bioenergy landscape and the logistics networks needed for the biofuel supply chain. Typical studies of the scale, cost, and greenhouse gas (GHG) mitigation potential of cellulosic biofuel take a land-centered approach which may neglect to account for the trade-offs between establishing bioenergy crops and the supply chain design decisions needed to allow those crops to be converted to liquid fuel. A mathematical programming approach is used to minimize the total annualized cost of a large-scale field-to-product system producing bioethanol in the USA midwest. Results show that a high concentration of marginal land leads to efficient systems and that the bioenergy landscape design becomes increasingly important with a higher emphasis on GHG mitigation. Additionally, targeted landscape design (including fertilization) with a focus on fields with high soil carbon sequestration potential can greatly reduce the system-wide GHG emissions for only a small increase in the unit cost of biofuel.

09 BIOMASS FUELS

Soil oxygen dynamics: a key mediator of tile drainage impacts on coupled hydrological, biogeochemical, and crop systems

Tile drainage removes excess water and is an essential, widely adopted management practice to enhance crop productivity in the US Midwest and throughout the world. Tile drainage has been shown to significantly change hydrological and biogeochemical cycles by lowering the water table and reducing the residence time of soil water, although examining the complex interactions and feedbacks in an integrated hydrology–biogeochemistry–crop system remains elusive. Oxygen dynamics are critical to unraveling these interactions and have been ignored or oversimplified in existing models. Understanding these impacts is essential, particularly so because tile drainage has been highlighted as an adaptation under projected wetter springs and drier summers in the changing climate in the US Midwest. We used the ecosys model that uniquely incorporates first-principle soil oxygen dynamics and crop oxygen uptake mechanisms to quantify the impacts of tile drainage on hydrological and biogeochemical cycles and crop growth in corn–soybean rotation fields. The model was validated with data from a multi-treatment, multi-year experiment in Washington, IA. The relative root mean square error (rRMSE) for the corn and soybean yield in validation is 5.66 % and 12.57 %, respectively. The Pearson coefficient (r) of the monthly tile flow during the growing season is 0.78. Plant oxygen stress turns out as an emergent property of the equilibrium between the soil oxygen supply and biological demand. The impact of tile drainage on the system is achieved through a series of coupled feedback mechanisms. The model results show that tile drainage reduces the soil water content and enhances soil oxygenation. It additionally increases the subsurface discharge and elevates inorganic nitrogen leaching, with seasonal variations influenced by climate and crop phenology. The improved aerobic condition alleviates crop oxygen stress during wet springs, thereby promoting crop root growth during the early growth stage. The development of greater root density, in turn, mitigates water stress during dry summers, leading to an overall increase in the crop yield by ∼6 %. These functions indicate the potential of tile drainage in bolstering crop resilience to climate change and the use of this modeling tool for large-scale assessments of tile drainage. The model reveals the underlying causal mechanisms that drive the agroecosystem response to drainage on the coupled hydrology, biogeochemistry, and crop system dynamics.

60 APPLIED LIFE SCIENCES

Linking Plant and Microbial Traits to Soil Carbon for Reliable and Resilient Bioenergy Systems

Bioenergy systems in the United States offer a dual opportunity to supply renewable feedstocks while enhancing ecosystem services such as hydrologic regulation, erosion control, and soil carbon (C) storage. National assessments highlight the potential to grow perennial energy crops to improve soil function and ecosystem resilience. Realizing this potential requires understanding the ecological mechanisms that govern how C is added, transformed, and stabilized in soils. Plant traits determine the quantity, depth, and chemistry of organic inputs, while microbial processes—including carbon use efficiency, necromass formation, and trophic interactions—mediate their transformation and partitioning among soil carbon pools. These biological pathways are shaped by soil physical and chemical properties, including aggregation, texture, and mineralogy, and by environmental drivers such as temperature, moisture, and disturbance, leading to context-dependent outcomes across landscapes. Management practices that diversify feedstocks, minimize disturbance, and maintain soil cover can promote both biomass production and C retention, while microbial amendments and rhizosphere engineering offer emerging, but often context-dependent, tools to optimize plant–microbe interactions. Trade-offs between biomass yield and soil carbon storage may arise when systems favor rapid aboveground productivity at the expense of belowground inputs and microbial processing, underscoring the importance of trait combinations that support both functions. Advances in monitoring, reporting, and verification—spanning precision agriculture, remote sensing, and biosensing—are improving predictive capacity through microbial-explicit process models and model–experiment (ModEx) frameworks. By connecting soil, plant, and microbial processes with advances in modeling and biosensing, this review outlines research priorities focused on trait-based parameterization and ModEx integration. These priorities will support the design of bioenergy systems that are both reliable and resilient, enhancing renewable energy production and ecosystem sustainability.

bioenergy systems

Plant Design for a Developing Bioeconomy Workshop Report: Frontier Science for the Bioeconomy Workshop Series

Recent advances in fundamental plant biology research, synthetic biology, and artificial intelligence (AI) are unlocking powerful new capabilities in plant biodesign, offering unprecedented potential to reimagine plants as programmable platforms for resource-efficient production of bioenergy, biomaterials, chemicals, and more. The U.S. Department of Energy (DOE) convened the Plant Design for a Developing Bioeconomy virtual workshop on March 12 through 14, 2025, to bring together leaders across plant science, engineering, and computation to assess the current landscape and define a bold vision for future research. Discussions during the workshop built upon findings included in DOE’s Biological and Environmental Research (BER) workshop report Overcoming Barriers in Plant Transformation: A Focus on Bioenergy Crops (U.S. DOE 2024; genomicscience. energy.gov/plant-transformation). Participants identified critical knowledge gaps, technical barriers, and emerging opportunities in the design and engineering of plant systems to support a robust, resilient domestic bioeconomy aligned with DOE’s mission.

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Agent-based Modeling for the Multi-objective Optimization of Energy Production Pathways: Integrated Techno-Economics and Life Cycle Assessment

This project developed an integrated modeling framework to evaluate how purpose-grown bioenergy feedstocks could support large-scale sustainable aviation fuel production in the United States. Led by Colorado State University with project partners, the work combined geographically resolved analysis, techno-economic assessment, life cycle assessment, multi-objective optimization, and agent-based modeling to examine feedstock performance, deployment potential, land-use implications, and adoption dynamics. The overall goal was to identify practical and sustainable pathways for producing aviation fuel from feedstocks such as energy crops, woody crops, oilseeds, and algae while helping inform policy, investment, and research needs tied to national SAF goals. In essence, the project provides a systems-level assessment of the opportunities and constraints associated with scaling bioenergy-based aviation fuels in the U.S.

09 BIOMASS FUELS

Leveraging hyperspectral phenotyping for accurate, non-destructive prediction of metabolite profiles in poplar under drought stress

Accurately predicting drought tolerance in woody perennial bioenergy crops is critical for sustainable biomass production under fluctuating precipitation. Hyperspectral imaging (HSI) in the visible-near-infrared (VNIR) and shortwave-infrared (SWIR) ranges offers a promising approach for predicting plant biochemical traits, yet its application in metabolite profiling remains underexplored. We integrated VNIR+SWIR HSI with untargeted metabolomics to investigate drought-induced metabolic shifts in Populus leaves from eight Populus genotypes. Metabolite profiling identified 127 compounds, with 73 showing significant drought responses spanning amino acids (AA), carbohydrates (CHO), phenolic glycosides (PG), organic acids (OA), fatty acids and alcohols (FA), terpenes (T), phenolic metabolites (P), and unclassified metabolites. Spectral analysis revealed consistently higher reflectance across VNIR and SWIR wavelengths in drought-stressed plants, corresponding with increased accumulation of AA and reduced CHO and PG levels. Least absolute shrinkage and selection operator (LASSO) regression modeling identified robust spectral predictors of metabolite concentrations, associating VNIR wavelengths (500–700 nm) predominantly with AA and P, whereas SWIR wavelengths (1680–1700 nm) reliably predicted CHO, OA, and T. Several stable spectral-metabolite associations persisted across the two watering regimes (drought vs. well-watered), highlighting their potential as spectral biomarkers for non-destructive stress monitoring. Minimal genotype-specific variation suggests that observed spectral and metabolic responses were driven primarily by environmental factors, likely reflecting limited genetic diversity among the commercial Populus genotypes examined. This work establishes VNIR+SWIR hyperspectral imaging as a powerful, non-destructive phenotyping tool for precision monitoring and targeted improvement of drought resilience in bioenergy crops.

Biochemical trait prediction

Rhizosphere Microbiome Diversity Potentially Supports Robust Nature of Field Pennycress ( Thlaspi arvense L.) in Dryland Cropping Systems of Eastern Washington

ABSTRACT Field pennycress ( Thlaspi arvense L.) is an annual in the Brassicaceae family and is currently being developed as an oilseed intermediate crop suitable for renewable biodiesel and jet fuel. It displays many desirable characteristics for this role including cold tolerance, a rapid life cycle, and a seed fatty acid profile conducive to bioenergy generation. These traits make field pennycress favorable for winter oilseed cultivation in the inland Pacific Northwest (iPNW). Simultaneously, intermediate crops are an increasingly recognized component of both agronomic sustainability and soil health management. Intermediate crops enhance soil microbial diversity, which benefits both soil and plant health. To understand the impact of field pennycress on soil microbial diversity, two natural accessions and seven experimental accessions were grown at three sites in Eastern Washington. Aboveground biomass and rhizosphere soil were then collected. Soil genomic DNA was extracted from rhizosphere samples and used to generate an amplicon library for bacterial (16S) and fungal (ITS) rRNA sequences. The resulting libraries were analyzed in QIIME2, which revealed that not only did the fad2 deficient line from the Spring32‐10 background have significantly increased aboveground biomass production compared to other pennycress genotypes, but also displayed significantly higher β‐diversity in the rhizosphere community specifically at the site experiencing the driest conditions. ANCOM analysis showed that multiple sequences similar to beneficial plant and soil health enhancing organisms such as Trichoderma spirale , Pseudomonas spp., and Methylobacterium goesingense were found to be enriched in the microbiome of the fad2 Spring32‐10 background also at that site. To add additional context to rhizosphere community data, root exudates from two pennycress genotypes were captured in magenta boxes and analyzed using HPLC. Future work will expand our understanding of the mechanisms by which field pennycress creates diversity in the rhizosphere, thus expanding our ability to cultivate this crop in the iPNW.

54 ENVIRONMENTAL SCIENCES

Optimization for Bioenergy Systems

The Sustainable Aviation Fuel (SAF) Grand Challenge (Langholtz, 2024 ) seeks to generate 35 billion gallons of SAF each year by 2050, with corn stover, an agricultural byproduct, playing a key role as a feedstock. This study develops an optimization framework to enhance the quality and quantity of corn stover while ensuring economic and environmental viability. Using the Decision Support System for Agrotechnology Transfer (DSSAT) crop model, we simulate the effects of cover crops on rotation yield, soil moisture balance, and nitrogen cycling across diverse climates and soils. The model outputs, including yield data and soil quality changes, inform a Mixed-Integer Linear Programming (MILP) optimization model. This model aims to maximize economic and environmental returns by incorporating production costs, direct and indirect income, and environmental incentives. The optimization model evaluates 280 agriculture management plans composed of various crop management strategies, including corn stover removal rates, cover crop adoption, and fertilization practices. It seeks to identify the optimal combination of crop and tillage decisions for each subfield, maximizing profits while enhancing soil carbon sequestration and reducing greenhouse gas emissions. Outputs include detailed subfield locations, optimal management plans, and profits per hectare and per acre, allowing for comparison with literature values on farm profits. This study provides a robust optimization framework supporting the SAF Grand Challenge by proposing economically viable and environmentally sustainable strategies for corn stover utilization. The findings highlight corn stover's potential as a sustainable feedstock for SAF production, offering practical solutions to enhance its quality and quantity while maintaining soil health. Idaho is used as a case study to demonstrate the framework's applicability and effectiveness in real-world scenarios. Langholtz, M. H., Davis, M., Hellwinckel, C., De La Torre Ugarte, D., Efroymson, R., Jacobson, R., Milbrandt, A., Coleman, A., Davis, R., Kline, K. L., Badgett, A., Curran, S., Schmidt, E., Theiss, T., Fried, J., English, B., Lambert, L., Cook, H., Field, J., ... Walker, L. (2024). 2023 Billion-Ton Report: An Assessment of U.S. Renewable Carbon Resources. https://doi.org/10.2172/2441098 DSSAT Foundation. (2025). Decision Support System for Agrotechnology Transfer (DSSAT). Retrieved from https://dssat.net/

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