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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Virulence and Genetic Diversity of Puccinia spp., Causal Agents of Rust on Switchgrass (Panicum virgatum L.) in the USA

Switchgrass (Panicum virgatum L.) is an important cellulosic biofuel grass native to North America. Rust, caused by Puccinia spp. is the most predominant disease of switchgrass and has the potential to impact biomass conversion. In this study, virulence patterns were determined on a set of 38 switchgrass genotypes for 14 single-spore rust isolates from 14 field samples collected in seven states. Single nucleotide polymorphism (SNP) variation was also assessed in 720 sequenced cloned amplicons representing 654 base pairs of the elongation factor 1-α gene from the field samples. Five major haplotypes were identified differing by 11 out of the 39 SNP positions identified. STRUCTURE, Principal Coordinate Analysis, and phylogenetic analyses divided the rust population into two genetic clusters. Virginia and Georgia had the highest and lowest rust genetic diversity, respectively. Only nine accessions showed a differential disease response between the 14 isolates, allowing the identification of eight races, differing by 1–3 virulence factors. Overall, the results suggested clonal reproduction of the pathogen and a North–South differentiation via local adaptation. However, similar haplotypes and races were also recovered from several states, suggesting migration events, and highlighting the need to further investigate the switchgrass rust population structure and evolution in the USA.

Bahri, Bochra A. (ORCID:0000000159055880)↗
DOE OSTI2025

Switchgrass Best Management Practices for Biofuel Production

Switchgrass is a perennial C 4 grass native to North America and broadly adaptable across the U.S. Its high productivity, low input requirements, and ability to deliver significant ecosystem services benefits, including carbon sequestration, soil conservation, and wildlife habitat, make it well-suited for cultivation on marginal lands. Achieving the U.S. Department of Energy’s projected potential of 1 billion dry tons of biomass annually by 2050 – with switchgrass contributing up to 230 million tons – will require a transition to large-scale, commercial production. This technical guide was developed to provide decision-makers with current best management practices (BMPs) for establishing, managing, and harvesting bioenergy switchgrass at scale on marginal lands across the U.S. Midwest and Great Plains. Drawing extensively on previous field research and insights from the five-year 'Next-Generation Feedstocks for the Emerging Bioeconomy' project – funded by the U.S. Department of Energy’s Bioenergy Technologies Office – this guide provides practical strategies for scaling up switchgrass production to meet the demands of the growing bioeconomy.

Lee, D.K.↗
DOE OSTI2025

Developmentally-specific physiological and metabolic responses support drought resilience in switchgrass and constrains biofuel yield

Switchgrass (Panicum virgatum) is a promising bioenergy crop due in part to its resilience to drought stress. However, the significance of drought timing remains poorly understood, both from a plant biology perspective and its impact on downstream biofuel production. This study determines the developmental stage-specific physiological and metabolic responses of switchgrass to drought stress and its implications for biofuel production using a custom-built programmable irrigation system. Vegetative, flowering, and senescence-stage drought significantly reduced carbon dioxide assimilation, and stomatal conductance without affecting biomass yield. Metabolic profiling revealed significant accumulation of glucose, fructose, quinic acid, shikimate and GABA during vegetative-stage drought, while flowering and senescence stages exhibited limited metabolic changes. Similarly, specialized metabolites also displayed distinct developmental patterns, with vegetative-stage drought driving the most pronounced metabolic alterations. Thermochemically-treated and hydrolyzed switchgrass biomass from vegetative-stage drought showed elevated lignocellulose-derived compounds and saponins with the latter most positively correlating with fermentation lag times. Conversely, senescence-stage drought enhanced ethanol yields while lowering saponin levels in the hydrolysates. While vegetative-stage drought enhanced physiological resilience, it compromises downstream biofuel production by introducing fermentation inhibitors, particularly saponins.

biofuel↗
DOE OSTI2025

Local adaptation of both plant and pathogen: an arms‐race compromise in switchgrass rust

In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes. To better understand local adaptation in host–parasite systems, we examined locally adapted switchgrass (Panicum virgatum), and its leaf rust pathogen (Puccinia novopanici) across a latitudinal range in North America. We grew switchgrass genotypes in 10 replicated multiyear common gardens, measuring rust severity from natural infection in a ‘host reciprocal transplant’ framework for testing local adaptation. We conducted genome-wide association mapping to identify genetic loci associated with rust severity. Genetically differentiated rust populations were locally adapted to northern and southern switchgrass, despite host local adaptation to environmental conditions in the same regions. Rust resistance was polygenic, and distinct loci were associated with rust severity in the north and south. We narrowed a previously identified large-effect quantitative trait locus for rust severity to a candidate YELLOW STRIPE-LIKE gene and linked numerous other loci to defense-related genes. Overall, our results suggest that both hosts and parasites can be simultaneously locally adapted, especially when parasites impose less selection than other environmental factors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Impact of Storage Conditions on the Quality and Viability of Switchgrass as a Bioenergy Crop

With growing energy demands and climate concerns, advancements in bioenergy have become imperative. Biofuels promote energy independence, reduce fossil fuel reliance, and cut greenhouse gas emissions. Switchgrass (Panicum virgatumis) is an ideal bioenergy crop due to its ability to thrive on marginal lands unsuitable for food crops and its drought tolerance, rendering it a low-maintenance, high-yield option. In the bioenergy industry, energy crops are typically stored to facilitate supply chain management and ensure a continuous supply despite seasonal availability. However, the effective utilization of bioenergy crops is typically contingent upon addressing the challenges associated with biomass storage. These challenges include high moisture content that promotes biological degradation of the biomass leading to increased risk of pathogenic microbes, and chemical degradation that increases the ratio of inconvertible, inorganic materials. These issues lead to a reduction of feedstock value, diminishing the biomass-to-biofuel conversion efficacy, making switchgrass and other bioenergy crops less effective as fuel sources. This project aims to improve the storage of purpose-grown energy crops. Aerobic storage trials were conducted under varying moisture contents to stimulate real-world environmental exposure. Switchgrass samples were rewetted to 30% or 35% and stored in a bioreactor for approximately one month, or until cellular respiration ceased. Degradation indicators, such as dry matter loss, temperature changes, and cellular respiration, were measured throughout this process. Samples for compositional analysis, 16S, and ITS were taken at three different time points: before, during, and after storage, to monitor changes in biomass, microbial communities, and metabolites over time. Preliminary data indicate that dry matter loss is proportional to cellular respiration, with higher moisture content (35%) leading to higher temperatures and elevated dry matter loss. Compositional analysis and microbial community analysis are in progress. This research will provide a comprehensive understanding of storage, helping to identify stability factors in energy crops and improve best management practices for biomass producers.

09 - BIOMASS FUELS↗
DOE OSTI2025

Life Cycle Emissions and Health Cost Impacts of Producing Ethanol and Electricity from Willow and Switchgrass in the Riparian Buffers of Mid-Atlantic United States

The United States (US Mid-Atlantic Region (MAR) has the potential to grow a variety of perennial feedstocks such as switchgrass and shrub willow to increase domestic energy production. These cellulosic feedstocks have also shown improved ecosystem services, such as soil carbon sequestration, nitrate leaching reduction, and flood mitigation along rivers and streams as partially harvested riparian buffers. To examine the effects on greenhouse gases (GHGs) and criteria air pollutants (CAPs) from using these feedstocks to produce ethanol or electricity, we conducted a comprehensive life cycle assessment (LCA) and estimated the impact on human health costs when land use is changed from corn production for ethanol. Results indicate up to 54% reduced GHG per hectare from using willow and switchgrass feedstock sources to produce ethanol instead of corn. However, there was a trade-off in terms of CAP emission, as grass-based energy emitted more NO x and SO x compared to the corn ethanol pathway, except for SO X emissions from willow-based electricity. Electricity from cellulosic biomass had higher particulate matter (PM) emission compared to that from corn ethanol. Estimates for health cost to society ranged from $2498 ha –1 for electricity from switchgrass to a net benefit of $448 ha –1 for ethanol production from willow, depending on varying biomass yield under different market scenarios. Although using cellulosic feedstocks to produce bioenergy has great potential to reduce GHG emissions, CAP control measures are needed to manage CAP-induced health costs.

Bioenergy↗
DOE OSTI2025

Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass

Genomic prediction has accelerated breeding processes and provided mechanistic insights into the genetic bases of complex traits. To further optimize genomic prediction, we assess the impact of genome assemblies, genotyping approaches, variant types, allelic complexities, polyploidy levels, and population structures on the prediction of 20 complex traits in switchgrass (Panicum virgatum L.), a perennial biofuel feedstock. Surprisingly, short read-based genome assembly performs comparably to or even better than long read-based assembly. Due to higher gene coverage, exome capture and multi-allelic variants outperform genotyping-by-sequencing and bi-allelic variants, respectively. Tetraploid models show higher prediction accuracy than octoploid models for most traits, likely due to the greater genetic distances among tetraploids. Depending on the trait in question, different types of variants need to be integrated for optimal predictions. Furthermore, our study provides insights into the factors influencing genomic prediction outcomes, guiding best practices for future studies and for improving agronomic traits in switchgrass and other species through selective breeding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Drought adaptation index (DAI) based on BLUP as a selection approach for drought-resilient switchgrass germplasm

This study introduces a Drought Adaptation Index (DAI), derived from Best Linear Unbiased Prediction (BLUP), as a method to assess drought resilience in switchgrass (Panicum virgatum L.). A panel of 404 genotypes was evaluated under drought-stressed (CV) and well-watered (UC) conditions over four consecutive years (2019–2022). BLUP-estimated biomass yields were used to calculate the DAI, which enabled classification of genotypes into four adaptation groups: very well-adapted, well-adapted, adapted, and unadapted. The DAI was compared with conventional drought tolerance indices, including the Stress Susceptibility Index (SSI), Stress Tolerance Index (STI), Geometric Mean Productivity (GMP), and Yield Stability Index (YSI). Correlation analyses demonstrated strong agreement between DAI and these indices, supporting its validity and consistency. Biplot analyses using the Genotype plus Genotype-by-Environment Interaction (GGE) and Additive Main Effects and Multiplicative Interaction (AMMI) models revealed significant genotype-by-environment interactions (GEI) and identified J222.A, J463.A, and J295.A. A as high-performing genotypes, with J222.A exhibiting greater yield stability across treatments and years. Additionally, DAI isoline curves provided a graphical representation of differential genotype performance under drought and control conditions. These visualizations aided in distinguishing genotypes with stable and superior biomass yield across contrasting environments. Overall, the BLUP-based DAI is a robust and practical selection tool that improves the accuracy of identifying drought-resilient, high-yielding switchgrass genotypes. Its integration into breeding programs offers a comprehensive framework for improving biomass productivity and stress adaptation under variable climatic conditions. The application of DAI supports the development of climate-resilient cultivars and contributes to sustainable bioenergy and forage production systems.

BLUP↗
DOE OSTI2024

Pore Structures in Detritusphere of Soils Under Switchgrass and Restored Prairie Vegetation Community

Root detritusphere, that is, the soil in the vicinity of decomposing root residues, plays an important role in soil microbial activity and C sequestration. Pore structure (size distributions and connectivity of soil pores) in the detritusphere serves as a major driver for these processes and, in turn, is influenced by the physical characteristics of both soil and roots. This study compared pore structure characteristics in the root detritusphere of soils of contrasting texture and mineralogy subjected to > 6 years of contrasting vegetation: monoculture switchgrass and polyculture prairie systems. Soil samples were collected from five experimental sites in the US Midwest representing three soil types. Soil texture and mineralogy were measured using a hydrometer and x-ray powder diffraction, respectively. The intact cores were scanned with x-ray computed micro-tomography to identify visible soil pores, biopores, and particulate organic matter (POM). We specifically focused on pore structure within the detritusphere around the POM of root origin. Results showed that the detritusphere of coarser textured soils, characterized by high sand and quartz contents, had lower porosity in the vicinity of POM compared with finer textured soils. POM vicinities in finer textured soils had high proportions of large (> 300 μm diameter) pores, and their pores were better connected than in the coarser soils. Lower porosity in the outer (> 1 mm) parts of the detritusphere of switchgrass than of prairie suggested soil compaction by roots, with the effect especially pronounced in the coarser soils. Here, the results demonstrated that soil texture and mineralogy played a major, while vegetation played a more modest, role in defining the pore structure in the root detritusphere.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Microbial O 2 consumption as a function of pore structure in soils of sorghum, switchgrass, and prairie vegetation systems

Abstract Microscale O 2 availability in soil, a main factor influencing microbial processing of soil carbon and nitrogen, is a function of O 2 diffusion and microbial O 2 consumption. While O 2 diffusivity is widely studied, it is difficult to quantify the rate of microbial O 2 consumption ( MO ). In this study, we quantified the MO using O 2 microsensor profiling to compare MO in different soils and vegetation systems while manipulating the soil pore structure. Soil samples were collected from three bioenergy vegetation systems, sorghum ( Sorghum bicolor L. Moench), switchgrass ( Panicum virgatum L.), and prairie, at an experimental site in Southeast Michigan, and from switchgrass and prairie systems at two sites in South and North Wisconsin. We prepared soil cores with two contrasting pore structures, that is, large (>30 µm Ø) pore‐dominated soil (LP) and small (<10 µm Ø) pore‐dominated soil (SP), from the same 1‐ to 2‐mm soil size fraction. We quantified MO (nmol O 2 cm −3 s −1 ) using a microprofiler with an oxygen (OX‐100 µm) microsensor (Unisense) pre‐ and post‐38‐day incubation. Across all studied systems, there was a trend for a decrease in SP MO post‐incubation, suggesting a change in microbial metabolism to lower O 2 utilization. However, sizeable microbial O 2 consumption continued in the LP soils, further corroborated by a positive correlation between the C‐CO 2 emission rate and the post‐incubation MO , highlighting that LP provided a better physical microenvironment for the soil microbes.

Chakraborty, Poulamee [Department of Plant Soil an↗
DOE OSTI2025

Root architectural plasticity optimizes nutrient acquisition in switchgrass under variable phosphorus forms

Aims Understanding the influence of different forms of phosphorus (P) over the different root traits and how those traits are related to increasing the efficiency of nutrient acquisition strategies. Methods Investigation of switchgrass (Panicum virgatum L.) root morphology responses to inorganic P (Pi) soluble (Potassium-P), insoluble (Aluminum-P), and organic P (Po) (Inositol Hexa-Phosphate, IHex-P) in rhizoboxes. Roots were traced over the root box and scanned using WinRhizoTM. The CRootbox model was employed to simulate root growth. Results Significant plasticity observed under IHex-P treatment, with a 46% increase in root branching, leading to a 74% rise in total root length and a 65% increase in root surface area compared to inorganic P forms. IHex-P resulted in a 73% higher root biomass than Aluminum-P and a 26% increase compared to Potassium-P. Most of the differences were attributed to the elongation of root branches. Conclusions Here, the study emphasizes the dynamic nature of switchgrass root architecture and morphology in response to varying P forms in the soil. The absence of Pi in the soil triggered increased plasticity in root traits, facilitating root access to Po and uptake of P. These findings offer valuable insights into the adaptive mechanisms of perennial plants, with significant implications for optimizing nutrient acquisition strategies in both agricultural and natural ecosystems.

Organic phosphorus↗
DOE OSTI2026

Novel Cell-Type-Specific Drought-Responsive Proteins in Root Tips of Field-Grown Perennial Switchgrass

The root-tip region of plants, including the root cap, forms the most basal terminal of the root and exhibits a high degree of cellular complexity in terms of morphology, cytological function, and interaction with environmental cues in the soil. Cells in this region follow a developmental trajectory, transitioning from stem cells to meristematic cells, and ultimately to fully differentiated cell types. However, our understanding of root-tip cell-type specific proteomic responses to abiotic stresses, such as drought, particularly under field conditions, remains limited. This study aimed to identify spatially resolved, cell type-specific proteomes in switchgrass (Panicum virgatum) root tips under drought stress. Root tips were collected from seven-year-old, field-grown switchgrass ‘Alamo’ plants excavated under both well-watered and long-term drought conditions. Cell type-specific proteins were identified using laser capture microdissection (LCM) coupled with nanoPOTS (Nanodroplet Processing in One Pot for Trace Samples) and nano-LC-MS proteomics analysis. Five distinct cell types were targeted: (1) cells in the quiescent center and stem cell niche (QuC), (2) protodermal epidermal cells (PEC) in the meristematic zone, (3) epidermal cells in the transition and elongation zones above the root cap (Epi), (4) peripheral root cap cells (PRC), forming 2–3 layers below the PEC and 1–2 layers above the root border cells, and (5) columella root cap cells (Col) comprising of the columella initials and a single underlying layer of cells undergoing active growth. Principal component analysis (PCA) revealed clear separation among the five targeted cell types, confirming distinct proteomic profiles. Proteins predominantly enriched in each cell type were linked to distinct cellular functions, with QuC cells showing involvement in chromosomal behavior, DNA replication, and mitosis—key processes for stem cell niche regulation. Drought stress resulted in alterations of proteostasis, as evidenced by significant decreases in ribosomal proteins and increases in protein synthesis inhibitors. Moreover, drought stress induced unique cell-type–specific proteins involved in phytohormone biosynthesis and signaling pathways, including auxin, cytokinin, and jasmonic acid. In particular, QuC cells were more highly enriched in proteins associated with DNA repair and mitotic processes. Metabolic pathways related to amino acids, carbohydrates, and lipids were differentially affected in a cell-type–dependent manner, whereas general stress-responsive proteins exhibited consistent changes across all five cell types. Overall, this study provides unique spatially resolved, cell-type-specific proteomic profiles in root tips, representing a significant advancement in our understanding of the cellular mechanisms underlying plant responses to drought stress in natural field conditions.

perennial grass↗
DOE OSTI2026

AmeriFlux FLUXNET-1F US-UiA University of Illinois Switchgrass

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-UiA University of Illinois Switchgrass. This is the FLUXNET version of the carbon flux data for the site US-UiA University of Illinois Switchgrass produced by applying the standard ONEFlux (1F) software. Site Description - Field was treated with Potash, lime and diammonium phosphate before planting. Herbicide application included 2,4-D for 2008, 2009. 56 kg/ha nitrogen applied in 2010, 2011, 2012, 2013, 2014, 2016. Measurements were suspended on June 14, 2016 and resumed on May 28, 2024.

Bernacchi, Carl↗
DOE OSTI2025

Draft genome of the switchgrass head smut pathogen Tilletia maclaganii V.2

The head smut (Tilletia maclaganii) is a significant pathogen of the bioenergy crop switchgrass. T. maclaganii typically is more prevalent in older stands of switchgrass and can contribute to significant biomass loss. Here, we outline the methods for the sequencing, assembly, and annotation of the first reference genome for Tilletia maclaganii.

Benucci, Gian Maria Niccolò [GLBRC - Michigan Stat↗
DOE OSTI2026

Root of the matter-Impacts of harvest frequency on soil C and nutrients in switchgrass

We evaluated how harvest frequency affected plant C allocation and soil-water nutrient concentrations in a switchgrass (Panicum virgatumL.) system on the Eastern Shore of Maryland, U.S.A. Switchgrass established in 2023 was harvested once (1Cut), twice (2Cut), or three times (3Cut) during the 2024 growing season to represent potential feedstock-management regimes for anaerobic digestion. Aboveground biomass was measured at each harvest, and root biomass distribution, root C stocks, and soil properties were assessed to 60 cm after the growing season. During 2025, rainfall-synchronized soil water collected with tension lysimeters was analyzed for dissolved inorganic nitrogen (DIN) and inorganic phosphate (Pi) concentrations.

09 BIOMASS FUELS↗
DOE OSTI2025

Estimating Switchgrass Biomass Yield and Lignocellulose Composition from UAV-Based Indices

Innovative methods for estimating commercial-scale switchgrass yields and feedstock quality are essential to optimize harvest logistics and biorefinery efficiency for sustainable aviation fuel production. This study utilized vegetation indices (VIs) derived from multispectral images to predict biomass yield and lignocellulose concentrations of advanced bioenergy-type switchgrass cultivars (“Liberty” and “Independence”) under two N rates (28 and 56 kg N ha –1 ). Field-scale plots were arranged in a randomized complete block design (RCBD) and replicated three times at Urbana, IL. Multispectral images captured during the 2021–2023 growing seasons were used to extract VIs. The results show that linear and exponential models outperformed partial least square and random forest models, with mid-August imagery providing the best predictions for biomass, cellulose, and hemicellulose. The green normalized difference vegetation index (GNDVI) was the best univariate predictor for biomass yield (R 2 = 0.86), while a multivariate combination of the GNDVI and normalized difference red-edge index (NDRE) enhanced prediction accuracy (R 2 = 0.88). Cellulose was best predicted using the NDRE (R 2 = 0.53), whereas hemicellulose prediction was most effective with a multivariate model combining the GNDVI, NDRE, NDVI, and green ratio vegetation index (GRVI) (R 2 = 0.44). These findings demonstrate the potential of UAV-based VIs for the in-season estimation of biomass yield and cellulose concentration.

09 BIOMASS FUELS↗
DOE OSTI2025

Borate-assisted alkaline extraction of hemicellulose from switchgrass with enhanced structural stability and purity

Valorization of non-cellulosic polysaccharides is crucial for enhancing the economic competitiveness of biorefinery processes. In this study, a mixture of boric acid and sodium hydroxide was employed to efficiently extract hemicellulose from holocellulose switchgrass. Borate-assisted alkaline extraction resulted in a higher xylan content (59.5 %) compared to conventional alkaline extraction. Here, the hemicellulose fractions derived from the borate-alkaline treatment exhibited a higher molecular weight (M w = 51.2 kDa) and a relatively lower degree of polydispersity (1.28), indicating improved structural stability. The presence of borate had a protective effect against chain scission, preserving glucuronic acid residues and increasing galactose content. Additionally, borate improved hemicellulose purity, with up to 74.1 % of the extracted hemicellulose being suitable for further enzymatic applications. Extended extraction time further enhanced hemicellulose recovery, reaching 97.9 % under NaOH/boric acid conditions while maintaining structural integrity, as confirmed by SEM, FTIR and 2D HSQC NMR analyses. These findings provide insights into the role of borate in optimizing hemicellulose extraction and improving its potential for bioconversion processes.

Borate alkaline↗