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DOE OSTI2022

Control of chloroplast degradation and cell death in response to stress

Chloroplasts are the sites of photosynthesis in plants and algae and, by extension, are essential for most life on Earth. Their maintenance is costly and complex due to the inherent photo-oxidative damage incurred by photosynthetic chemistry. Chloroplast degradation and cell death are mechanisms by which plants acclimate to such stress and serve a dual purpose: protecting cells and organs by removing reactive oxygen species-producing chloroplasts and redistributing nutrients to other tissues. Here I review recent progress in understanding the molecular mechanisms initiating and facilitating such degradation and show these are complex processes involving multiple pathways. Furthermore, due to the links to photosynthesis and nitrogen metabolism, there is great potential to manipulate these pathways to increase crop yield and quality under stressful environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

CRISPR/Cas9 editing of p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE 1 in maize alters phenolic metabolism, lignin structure, and lignin-first biomass processing

Valorization of lignocellulosic biomass for sustainable production of high-value chemicals is challenged by the complexity of lignin, a phenolic biopolymer. Beyond the classical lignin monomers derived from p-coumaryl, coniferyl, and sinapyl alcohol, grass lignins incorporate substantial amounts of monolignol p-coumarates that are produced by p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE (PMT). Here, the CRISPR/Cas9-mediated mutation of ZmPMT1 in maize enabled the design of biomass depleted in p-coumaroylated lignin and enriched in guaiacyl lignin. Lignin-first biorefining of stem biomass from zmpmt1 mutants by reductive catalytic fractionation (RCF) generated a lignin oil depleted in carboxylates and enriched in guaiacyl-derived alcohols, which are desirable substrates for bio-based polyurethane synthesis. Furthermore, the reported lignin engineering in maize is a promising strategy for designing a dual-purpose crop, providing both food and feed, along with a renewable feedstock for the production of plant-based chemicals.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Enzymes as parts in need of replacement - and how to extend their working life

Enzymes catalyze reactions in vivo at different rates and each enzyme molecule has a lifetime limit before it is degraded and replaced to enable catalysis to continue. Considering these rates together as a unitless ratio of catalytic cycles until replacement (CCR) provides a new quantitative tool to assess the replacement schedule of and energy investment into enzymes as they relate to function. Here, we outline the challenges of determining CCRs and new approaches to overcome them and then assess the CCRs of selected enzymes in bacteria and plants to reveal a range of seven orders of magnitude for this ratio. Modifying CCRs in plants holds promise to lower cellular costs, to tailor enzymes for particular environments, and to breed enzyme improvements for crop productivity.

Catalytic rate↗

DOE OSTI2021

Mineral nutrient signaling controls photosynthesis: focus on iron deficiency-induced chlorosis

Photosynthetic organisms convert light energy into chemical energy stored in carbohydrates. To perform this process, an adequate supply of essential mineral elements, such as iron, is required in the chloroplast. Because iron plays a crucial role during electron transport and chlorophyll formation, iron deficiency alters photosynthesis and promotes chlorosis, or the yellowing of leaves. Intriguingly, iron deficiency-induced chlorosis can be reverted by the depletion of other micronutrients [i.e., manganese (Mn)] or macronutrients [i.e., sulfur (S) or phosphorus (P)], raising the question of how plants integrate nutrient status to control photosynthesis. Here, in this work, we review how improving our understanding of the complex relationship between nutrient homeostasis and photosynthesis has great potential for crop improvement.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

How volatile isoprenoids improve plant thermotolerance

Volatile isoprenoids mainly include isoprene and monoterpenes, which improve the thermotolerance of the emitting plant by lowering reactive oxygen species (ROS) levels, preserving chloroplast membrane ultrastructure, maintaining photosynthesis and primary metabolism, inducing heat shock proteins, and preserving growth and development. Recent data showed that isoprenoids can act as signaling molecules to improve plant thermotolerance by altering related gene expression through Ca 2+ -mediated signaling pathways. Here, to promote further understanding of isoprenoid-mediated thermotolerance mechanisms, we review current understanding of isoprenoid-induced plant thermotolerance, along with new findings describing the corresponding underlying mechanisms and putative signaling pathways. This information is beneficial for the potential utilization of isoprenoids for enhancing crop tolerance to global warming either by enhancing the emission of isoprenoids or by using isoprenoid-inspired anti-high temperature agents.

Ca2+ signal↗

DOE OSTI2026

Rewiring the unfolded protein response for plant growth recovery after stress

The unfolded protein response (UPR) is a highly coordinated signaling network that alleviates endoplasmic reticulum (ER) stress, a condition induced by diverse environmental challenges in plants. Over the past two decades, substantial progress has been made in elucidating the genetic and molecular mechanisms of ER stress sensing and signal transduction in plants, largely through studies in the model plant Arabidopsis thaliana . These advances have established the UPR as a central regulator of proteostasis and underscored its broader relevance to plant growth and development and crop productivity under stress conditions. Despite this progress, critical knowledge gaps remain, particularly concerning the downstream biological processes required for growth recovery once ER stress has subsided and how these processes are coordinated by UPR regulators. Recent systems-level and integrative studies have begun to reveal critical roles of UPR signaling in pathways governing growth re-establishment and homeostasis of nutrient allocation and energy metabolism. In this review, we highlight recent findings on the functional roles of the plant UPR in recovery from ER stress, with a focus on mechanisms mediated by UPR regulators and downstream biological pathways that enable the transition from stress mitigation to growth restoration. Although this research area is still emerging, accumulating evidence supports a model in which the UPR functions as a dynamic regulatory network that actively coordinates post-stress physiological recovery to support plant fitness.

ER stress↗

DOE OSTI2022

Significance of application timing, formulation, and cytochrome P450 genotypic class on sweet corn response to dicamba

Sweet corn (Zea mays L.) tolerance to dicamba and several other herbicides is due to cytochrome P450 (CYP)-mediated metabolism and is conferred by a single gene (Nsf1). Tolerance varies by CYP genotypic class, with hybrids homozygous for functional CYP (Nsf1Nsf1) being the most tolerant and hybrids homozygous for mutant CYP alleles (nsf1nsf1) being the least tolerant. The herbicide safener cyprosulfamide (CSA) increases tolerance to dicamba by stimulating the expression of several CYPs. However, the extent to which CSA improves the tolerance of different sweet corn CYP genotypic classes to dicamba is poorly understood. Additionally, the effect of growth stage on sweet corn sensitivity to dicamba is inadequately described. The objective of this work was to quantify the significance of application timing, formulation, and CYP genotypic class on sweet corn response to dicamba. Hybrids representing each of the three CYP genotypes (Nsf1Nsf1, Nsf1nsf1, nsf1nsf1), were treated with dicamba or dicamba + CSA at one of three growth stages: V3, V6, or V9. Across all timings, the nsf1nsf1 hybrid was the least tolerant to dicamba, displaying 16% higher crop injury levels 2 wk after treatment and 2,130 kg ha -1 lower ear mass yields compared with the Nsf1Nsf1 hybrid. The V9 growth stage was the most susceptible time for dicamba injury regardless of genotypic class, with 1.89 and 1,750 kg ha -1 lower ear mass yields compared with the V3 and V6 application timings, respectively. The addition of CSA to dicamba V9 applications reduced the injury from dicamba for all three genotypic classes; however, it did not eliminate the injury. The use of Nsf1Nsf1 or Nsf1nsf1 sweet corn hybrids along with herbicide safeners will reduce the frequency and severity of injury from dicamba and other CYP-metabolized herbicides.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications

Agriculture is under pressure to provide food for a growing population and the feedstock required to drive the bioeconomy. Methods to breed and genetically modify plants are inadequate to keep pace. When engineering crops, traits are painstakingly introduced into plants one-at-a-time, combine unpredictably, and are continuously expressed. Synthetic biology is changing these paradigms with new genome construction tools, computer aided design (CAD), and artificial intelligence (AI). “Smart plants” contain circuits that respond to environmental change, alter morphology, or respond to threats. Further, the plant and associated microbes (fungi, bacteria, archaea) are now being viewed by genetic engineers as a holistic system. Historically, plant health has been enhanced by many natural and laboratory-evolved soil microbes marketed to enhance growth, provide nutrients, or confer pest/stress resistance. Synthetic biology has expanded the number of species that can be engineered, increased the complexity of engineered functions, controlled environmental release, and assembled stable consortia. New CAD tools will manage genetic engineering projects spanning multiple plant genomes (nucleus, chloroplast, mitochondrion) and the thousands of genomes of associated bacteria/fungi. Here, this review covers advanced genetic engineering techniques to drive the next agricultural revolution, as well as push plant engineering into new realms for manufacturing, infrastructure, sensing, and remediation.

Clauer, Phillip [Massachusetts Inst. of Technology↗

DOE OSTI2025

Life-Cycle Emissions and Human Health Implications of Multi-Input, Multi-Output Biorefineries

To meaningfully broaden the supply of fuels for the transportation sector, biofuel production must be scaled up and this requires a wider array of biomass feedstocks, including agricultural residues and organic waste. Rather than pursuing conversion of lignocellulosic biomass to fuels and anaerobic digestion of wastes as separate pathways, there are economic and environmental advantages associated with integrating these processes in a single facility. However, existing research rarely goes beyond carbon footprints in quantifying the effects of such a shift in bioenergy production. In addition to CO2, CH4, and N2O, this study explores the life-cycle air pollution (NH3, volatile organic compounds, NOx, SO2, and PM2.5), marine eutrophication, acidification, and local external cost implications of biorefineries capable of taking in crop residues, food waste, and manure to produce liquid fuel, electricity, and/or other options such as renewable natural gas (RNG), hydrogen, bioplastics, and protein-rich livestock feed. Relative to a single-input, single-output baseline, biorefineries integrated with organic waste codigestion to coproduce electricity or RNG can reduce life-cycle CO2-equivalent emissions by 84-149%, and the monetized external impacts across all scenarios range from $1.07/gallon to -$0.75/gallon ethanol.

Air pollution↗

DOE OSTI2026

Optimizing Cryo-Focused Pyrolysis GC/MS for Tracing Soil Organic Matter Across Diverse Ecosystems

The cycling of organic matter in terrestrial soils and sediments is central to a range of biogeochemical processes that regulate nutrient cycling, crop productivity, trace gas emissions, and contaminant transport. Pyrolysis-gas chromatography/mass spectrometry (py-GC/MS) is a powerful tool for characterizing bulk soil organic matter (SOM) at the molecular level. In this study, we used a cryo-focused py-GC/MS system to analyze soil samples from seven diverse ecosystems: vernal pool, prairie pothole, temperate forest, tropical forest, tundra, wildfire-affected boreal forest, and grassland. We addressed a key bottleneck in molecular-level SOM characterization by developing an automated data analysis pipeline to optimize py-GC/MS and complementary evolved gas analysis/mass spectrometry (EGA/MS) methods, incorporating advanced tools for peak deconvolution, developing a custom compound class library, and implementing fragmentation spectrum-based molecular networking for the first time. This improved workflow was applied to soil samples from all seven ecosystems, including multiple depths and density fractions. Our findings demonstrate that ecosystem type plays a dominant role in shaping compositional differences in SOM. We also identified trends in the source of SOM compounds (e.g., microbial vs plantderived) across soil depth and density fractions, which are critical for understanding persistence and turnover of SOM. Our molecular networking analysis indicated that although many compounds are widespread across ecosystems, others are restricted to specific environments, such as wetlands. This underscores the utility of molecular-level data in elucidating the complexity of SOM composition and the environmental drivers that shape it. Such molecular-level insights can deepen our knowledge of biogeochemical SOM cycles.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Balancing Water Sustainability and Productivity Objectives in Microalgae Cultivation: Siting Open Ponds by Considering Seasonal Water-Stress Impact Using AWARE-US

Microalgae have great potential as an energy crop. Scaling-up algal biofuel production in the United States (US) should be done with careful attention to water stress. This study evaluates the regional and seasonal water-stress impact of potential algae-pond deployments in the US. Three site-selection strategies focusing on biomass yield, water-use efficiency (WUE), and water-stress impact, respectively, are applied and compared to meet a US algae biomass production target of 30 million metric tons/yr ash-free dry weight, which converts to 20.8 billion L renewable diesel, via hydrothermal liquefaction. Ranking algae ponds based on biomass yield leads to freshwater consumption of 2.66 km3/yr, resulting in the highest water-stress impact (39.1 US equivalent km3). Under the WUE scenario, water consumption is reduced by 81%, but biomass yield is reduced by 12%. In contrast, adding a water-stress constraint to the biomass-yield ranking reduces water consumption by 50% and water-stress impact by 97%, with a small yield reduction (1.7%). Results show that pond location has a significant effect on water stress and that water stress is not proportional to water consumption or yield. Furthermore, capturing seasonal water patterns is critical for planning because sites in water-abundant regions can have short-term but significant water-stress impacts.

algae, Biofuel, water scarcity footprint, hydrothe↗

DOE OSTI2020

Spatially and Temporally Explicit Life Cycle Environmental Impacts of Soybean Production in the U.S. Midwest

Quantifying the spatially and temporally explicit life cycle environmental impacts of crop production is critical for designing sustainable supply chains for biofuel and animal sectors. This study assessed life cycle environmental impacts of soybean production in around 1000 Midwest counties over 9 years. A combination of Environmental Policy Integrated Climate model and process-based life cycle assessment model was used to estimate the spatially and temporally explicit life cycle global warming (GW), eutrophication (EU) and acidification (AD) impacts. Sequentially, a machine learning approach was applied to identify the top influential factors among soil, climate and farming practices for spatially and temporally explicit life cycle environmental impacts. The results indicated that significant variations existed in life cycle environmental impacts among counties and across years. Life cycle GW impacts ranged from -11.4 to 22.0 kg CO2-eq. kg soybean-1, whereas life cycle EU and AD impacts varied by a factor of 302 and 44, respectively. Nitrogen application rates, temperature in March and soil texture were the top influencing factors for the spatial-temporal variations in life cycle GW impacts. In contrast, soil organic content and nitrogen application rate were the top influencing factors for the spatial-temporal variations in life cycle EU and AD impacts.

Soybean, life cycle analysis, sustainability, spat↗

DOE OSTI2020

Empirical Evidence for the Potential Climate Benefits of Decarbonizing Light Vehicle Transport in the U.S. with Bioenergy from Purpose-Grown Biomass with and without BECCS

Climate mitigation scenarios limiting global temperature increases to 1.5 °C rely on decarbonizing vehicle transport with bioenergy production plus carbon capture and storage (BECCS), but climate impacts for producing different bioenergy feedstocks have not been directly compared experimentally or for ethanol vs electric light-duty vehicles. A field experiment at two Midwest U.S. sites on contrasting soils revealed that feedstock yields of seven potential bioenergy cropping systems varied substantially within sites but little between. Bioenergy produced per hectare reflected yields: miscanthus > poplar > switchgrass > native grasses ≈ maize stover (residue) > restored prairie ≈ early successional. Greenhouse gas emission intensities for ethanol vehicles ranged from 20 to -179 g CO 2 e MJ –1 : maize stover $\gg$ miscanthus ≈ switchgrass ≈ native grasses ≈ poplar > early successional ≥ restored prairie; direct climate benefits ranged from ~80% (stover) to 290% (restored prairie) reductions in CO 2 e compared to petroleum and were similar for electric vehicles. With carbon capture and storage (CCS), reductions in emission intensities ranged from 204% (stover) to 416% (restored prairie) for ethanol vehicles and from 329 to 558% for electric vehicles, declining 27 and 15%, respectively, once soil carbon equilibrates within several decades of establishment. Extrapolation based on expected U.S. transportation energy use suggests that, once CCS potential is maximized with CO 2 pipeline infrastructure, negative emissions from bioenergy with CCS for light-duty electric vehicles could capture >900 Tg CO 2 e year –1 in the U.S. In the future, as other renewable electricity sources become more important, electricity production from biomass would offset less fossil fuel electricity, and the advantage of electric over ethanol vehicles would decrease proportionately.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Discovery of Novel Rhizoctonia solani DHFR Inhibitors as Fungicides Using Virtual Screening

Dihydrofolate reductase (DHFR) is an essential enzyme in the folate pathway and has been recognized as a well-known target for antibacterial and antifungal drugs. We discovered eight compounds from the ZINC database using virtual screening to inhibit Rhizoctonia solani (R. solani), a fungal pathogen in crops. These compounds were evaluated with in vitro assays for enzymatic and antifungal activity. Among these, compound Hit8 is the most active R. solani DHFR inhibitor, with the IC 50 of 10.2 μM. The selectivity of inhibition is 22.3 against human DHFR with the IC 50 of 227.7 μM. Moreover, Hit8 has higher antifungal activity against R. solani (EC 50 of 38.2 mg L –1 ) compared with validamycin A (EC 50 of 67.6 mg L –1 ), a well-documented fungicide. These results suggest that Hit8 may be a potential fungicide. Finally, our study exemplifies a computer-aided method to discover novel inhibitors that could target plant pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Gold-Nanocluster-Mediated Delivery of siRNA to Intact Plant Cells for Efficient Gene Knockdown

RNA interference, which involves the delivery of small interfering RNA (siRNA), has been used to validate target genes, to understand and control cellular metabolic pathways, and to use as a "green" alternative to confer pest tolerance in crops. Conventional siRNA delivery methods such as viruses and Agrobacterium -mediated delivery exhibit plant species range limitations and uncontrolled DNA integration into the plant genome. Here, we synthesize polyethylenimine-functionalized gold nanoclusters (PEI-AuNCs) to mediate siRNA delivery into intact plants and show that these nanoclusters enable efficient gene knockdown. We further demonstrate that PEI-AuNCs protect siRNA from RNase degradation while the complex is small enough to bypass the plant cell wall. Consequently, AuNCs enable gene knockdown with efficiencies of up 76.5 ± 5.9% and 76.1 ± 9.5% for GFP and ROQ1, respectively, with no observable toxicity. Our data suggest that AuNCs can deliver siRNA into intact plant cells for broad applications in plant biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Molecular Characterization of Organosulfate-Dominated Aerosols over Agricultural Fields from the Southern Great Plains by High-Resolution Mass Spectrometry

The molecular composition of organic aerosols, especially for day/nighttime variations of organosulfates above agricultural fields, is not well understood despite profound impacts on regional climate, crop production, air quality, and human health. Here, nanospray desorption electrospray ionization with high-resolution mass spectrometry (nano-DESI-HRMS) is used to interrogate the molecular composition of organic aerosols collected at the Southern Great Plains, located in an agricultural region of Oklahoma. Identified molecular formulae featured carbon, hydrogen, oxygen (CHO), nitrogen (CHNO), and/or sulfur (CHOS, CHNOS), with higher organosulfate proportions during daytime (41%) compared to nighttime (30%). In this work, nighttime aerosols featured increases in CHO, CHNO, and extremely low volatility organic carbon (ELVOC) species. However, due to high relative humidity, the nighttime aerosols phase state was found to be more liquid-like than daytime aerosols using parametrized glass transition temperatures. Aerosol molecular composition from an anthropogenically influenced plume (southerly winds) showed significant increases in CHOS and ELVOC species. By comparison with chamber studies, CHOS species are suspected to be of mixed biogenic and anthropogenic origin, whereas CHNOS species (not identified in the southerly winds) are suggested to predominately be of biogenic origin. Overall, this study provides key insight into organosulfates above agricultural fields, demonstrating dependence upon day/night cycles and episodic anthropogenic emissions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Harvest Initiated Volatile Organic Compound Emissions from In-Field Tall Wheatgrass

While crop and grassland usage continues to increase, the full diversity of plant-specific volatile organic compounds (VOCs) emitted from these ecosystems, including their implications for atmospheric chemistry and carbon cycling, remains poorly understood. It is particularly important to investigate VOCs in the context of potential biofuels: aside from the implications of largescale land use, harvest may shift both the flux and speciation of emitted VOCs. To this point, we evaluate the diversity of VOCs emitted both pre and postharvest from “Alkar” tall wheatgrass (Thinopyrum ponticum), a candidate biofuel that exhibits greater tolerance to frost and saline land compared to other grass varieties. Mature plants grown under field conditions (n = 6) were sampled for VOCs both pre- and postharvest (October 2022). Via hierarchical clustering of emitted VOCs from each plant, we observe distinct “volatilomes” (diversity of VOCs) specific to the pre- and postharvest conditions despite plant-to-plant variability. In total, 50 VOCs were found to be unique to the postharvest tall wheatgrass volatilome, and these unique VOCs constituted a significant portion (26%) of total postharvest signal. While green leaf volatiles (GLVs) dominate the speciation of postharvest emissions (e.g., 54% of unique postharvest VOC signal was due to 1-penten-3-ol), we demonstrate novel postharvest VOCs from tall wheatgrass that are under characterized in the context of carbon cycling and atmospheric chemistry (e.g., 3-octanone). Continuing evaluations will quantitatively investigate tall wheatgrass VOC fluxes, better informing the feasibility and environmental impact of tall wheatgrass as a biofuel.

09 BIOMASS FUELS↗

DOE OSTI2026

Rapid Evaluation of Amine-Functionalized Solvents for Biomass Deconstruction Using High-Throughput Screening and One-Pot Enzymatic Saccharification

Efficient and sustainable pretreatment of lignocellulosic biomass is critical for biofuel and biochemical production, yet its optimization is often hindered by slow, labor-intensive experimental methods. Here, we report the first demonstration of a custom-built, miniaturized, high-throughput screening platform integrated with one-pot enzymatic saccharification, enabling parallel evaluation of solvent type, feedstock, and temperature with minimal material use and high reproducibility. As a proof-of-concept, the HTX platform was used to screen five amine-functionalized solvents, including isopropanolamine, butylamine, N-methylbutylamine, ethanolamine, and ethanolamine acetate across three bioenergy crops (sorghum, poplar, and switchgrass) and pretreatment temperatures ranging from 80 to 140 °C. Vacuum drying successfully removed more than 99% of the solvents from the pretreated biomass, eliminating the need for water washing prior to saccharification. Isopropanolamine and N-methylbutylamine yielded the highest glucose (70–80%) and xylose (58–67%) release, with trends reflecting feedstock recalcitrance. The produced hydrolysates supported robust growth of an engineered strain of the yeast Rhodosporidium toruloides, confirming biocompatibility. This high-throughput platform provides a scalable, feedstock-agnostic framework for rapid pretreatment screening, accelerating solvent–feedstock pairing and process optimization. Its ability to integrate pretreatment, solvent removal, saccharification, and microbial conversion in a miniaturized format offers significant advantages for cost-competitive biorefinery development.

Biomass↗