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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Understanding and Harnessing the Robustness of Undomesticated Yarrowia lipolytica Strains for Biosynthesis of Designer Bioesters (Final Report)

This project seeks to elucidate and harness the exceptional robustness of novel and undomesticated Y. lipolytica isolates, which were identified from a genetic diversity screening for compatibility with bioenergy development. Bioenergy-relevant isolates were further developed as microbial platforms for efficient conversion of undetoxified biomass hydrolysates into designer bio-esters continuously recovered by solvent extraction. The project has three major goals. Goal 1. Elucidate and enhance the endogenous metabolism of Y. lipolytica for superior growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates under hypoxic conditions. Goal 2. Understand and enhance the underlying mechanism of exceptional tolerance of Y. lipolytica to organic solvents. Goal 3. Elucidate and rewire endogenous metabolism of the most robust Y. lipolytica strains for effective conversion of accumulating lipids to designer bio-esters. Significant progress has been made toward completing all research goals. We elucidated and optimized the robustness of Y. lipolytica by utilizing mixed C5 and C6 sugars in switchgrass hydrolysates (SGH) for lipid production (Aim 1). We conducted extensive omics analysis to investigate how genetic diversity among Yarrowia strains, derived from natural isolates or developed through adaptive laboratory evolution, influences lipid production when utilizing SGH. In Aim 2, novel mechanisms and underlying genetics were discovered that enabled Yarrowia strains to thrive in cultures containing high ionic liquid (IL) concentrations. Amongst other novel findings, it was found that sterols strengthened cell membranes to confer IL toxicity resistance, specifically via increased ergosterol content upon exposure to IL. In Aim 3, mechanistic studies elucidated how Y. lipolytica utilized intracellular lipids and alkanes/alkenes, leading to our discovery of novel enzymes and pathways for making short-chain esters. Most notably, thermostable chloramphenicol transferases were repurposed to function as alcohol acetyltransferases in Y. lipolytica, as well as the Gram-negative and Gram-positive bacteria Escherichia coli and thermophile Clostridium thermocellum, respectively.

09 BIOMASS FUELS↗
DOE OSTI2021

Comprehensive analysis of differentially expressed mRNA and circRNA in Ankylosing spondylitis patients’ platelets

Highlights: • 4996 mRNAs and 2942 circRNAs were identified differentially expressed in platelets of AS patients. • Several platelet-derived immune mediators were upregulated to regulate the interaction between platelets and immune cells. • Two downregulated circRNA were identified, and the corresponding circRNA-miRNA-mRNA regulatory network was constructed. • mRNAs and circRNAs found herein could be used as diagnostic biomarkers or new therapeutic targets. Ankylosing spondylitis (AS) is a chronic inflammatory disease significantly decreasing the quality of life. Platelets play an important and active role in the development of AS. Accumulating evidence demonstrated platelets contain diverse RNA repository inherited from megakaryocytes or microvesicles. Platelet RNAs are dynamically affected by pathological conditions and could be used as diagnostic or prognostic biomarkers. However, the role of the platelet RNAs in AS is elusive. In this study, we compared mRNA and circRNA profiles in platelets between AS patients and healthy controls using RNA sequencing and bioinformatic analysis, and found 4996 mRNAs and 2942 circRNAs were differently expressed. The significantly over-expressed mRNAs in AS patients are involved in platelet activity, gap junction, focal adhesion, rap1 and toll and Imd signaling pathway. The previous identified platelet-derived immune mediators such as P2Y1, P2Y12, PF4, GPIbα, CD40L, ICAM2, CCL5 (RANTES), TGF-β (TGF-β1 and TGF-β2) and PDGF (PDGFB and PDGFA) are also included in these over expressed mRNAs, implying these factors may trigger inflammatory cascades and promote the development of AS. Additionally, we found two down-regulated circRNA (circPTPN22 and circFCHSD2) from the intersection analyses of platelets and spinal ligament tissues of AS patients. The circRNA-miRNA-mRNA regulatory network of these two circRNAs was constructed, and the target mRNAs were enriched in Th17 cell differentiation, inflammatory bowel disease, cell adhesion molecules, cytokine-cytokine receptor interaction, Jak-STAT and Wnt signaling pathway, all these pathways participate in the bone remodeling and pro/anti-inflammatory immune regulation in AS. Then, qRT-PCR was performed to validate the expression of selected key mRNAs and circRNAs and the results demonstrated that the expression levels of P2Y12, GPIbα, circPTPN22 and circFCHSD2 were consistent with the sequencing analysis. In addition, the high expression of five predicted miRNAs interacting with circPTPN22 and circFCHSD2 were also detected in AS by qRT-PCR. Taken together, our study presents a comprehensive overview of mRNAs and circRNAs in platelets in AS patients and offers new insight into the mechanisms of platelet involving in the pathogenesis of AS. The mRNAs and circRNAs identified in this study may serve as candidates for diagnosis and targeted treatment of AS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Elucidating the Origins of High Capacity in Iron-Based Conversion Materials: Benefit of Complementary Advanced Characterization toward Mechanistic Understanding

Lithium-ion batteries are recognized as an important electrochemical energy storage technology due to their superior volumetric and gravimetric energy densities. Graphite is widely used as the negative electrode, and its adoption enabled much of the modern portable electronics technology landscape. However, developing markets, such as electric vehicles and grid-scale storage, have increased demands, including higher energy content and a diverse materials supply chain. Alternatives that provide the opportunity to increase capacity and address supply chain concerns are of interest. Understanding the fundamental mechanisms that govern battery function is crucial to driving further improvements in the field. Advanced characterization techniques, such as those enabled by synchrotron light sources and high-resolution electron microscopes, that can uncover these mechanisms have become a necessity for elucidating structural evolution upon electrochemical conversion at the nano- to mesoscales. Performing these experiments with relevant electrochemistry using in situ and operando experiments imparts the ability to identify critical reaction pathways and capture intermediate (dis)charge products not discernible by traditional experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Development of an All-Aqueous Thermally Regenerative Redox Flow Battery to Support Fossil Fuel Assets

Low-temperature thermal energy, a largely untapped resource, holds significant promise for large-scale electrical power generation globally. Various stationary sources, including industrial entities and thermal power plants, emit considerable low-temperature heat that currently remains unutilized. This energy is often overlooked because its low temperature renders it unsuitable for efficient power generation using conventional methods. However, current research is exploring diverse technologies capable of converting low-temperature heat into grid-scale power, aiming to enhance grid efficiency, further decarbonization initiatives, and facilitate a shift toward more decentralized power systems. One such innovative technology is the thermally regenerative battery (TRB), noted for its high power and energy densities compared to similar technologies, positioning it as a potential game-changer in power generation. TRBs integrate two scalable and well-established unit operations: a redox flow battery and a distillation column. This integration suggests that once an effective TRB chemistry is established, the pathway to commercialization could be expedited. The copper-based thermally regenerative ammonia battery (Cu aq -TRAB) stands out as the first TRB that circumvents electrodeposition/dissolution reactions, stabilizing Cu(I) and Cu(II) within the electrolyte and maintaining stability of all electroactive species in an aqueous phase. This stabilization has led to improvements in coulombic efficiency, open circuit potential, and copper solubility, thereby enhancing power density, energy density, and overall energy efficiency. Preliminary tests were conducted to determine the effects of various electrolyte species on the performance metrics of the battery, both theoretically and experimentally. These tests revealed that the solubility of copper in the Cu aq -TRAB electrolyte was constrained by the Cu(I)-NH 3 complex. Adjusting the background electrolyte to 5 M NH4Br and the ligand concentration to 4 M NH 3 enabled the copper concentration to reach a maximum of 0.6 M. This modification led to an estimated theoretical maximum energy density of 9.5 Wh L -1 for the Cu aq -TRAB. Additionally, full cell testing indicated a tradeoff between peak power and energy density with varying copper and ammonia concentrations. Increasing the applied current density during discharge linearly raised the average power output, with a minimal reduction in energy density due to a balance between higher ohmic overpotential and reduced time for undesirable ammonia crossover. Furthermore, a comprehensive numerical sensitivity analysis of the complete Cu aq -TRAB system was performed. This analysis aimed to assess how the battery and the distillation column responded to changes in system input parameters, providing insights into optimal research directions for enhancing system performance. The analysis revealed that at room temperature, battery power was significantly more sensitive to ohmic losses than to mass transfer, with reaction rates having minimal impact. This trend continued even at higher temperatures. Also, the thermal energy required for ammonia separation was studied, showing that increased temperatures generally reduced energy requirements, except in low-pressure scenarios above 65 °C. An investigation into membrane performance in the Cu aq -TRAB was undertaken, given the significant impact of ammonia transport control and ohmic losses on system performance. Various membranes were evaluated to identify key performance metrics. Among the tested membranes, Selemion CMVN exhibited the highest performance, with a peak power density of 84 mW cm -2 and average values of 26 ± 6.8 mW cm -2 for power density and 2.9 Wh L -1 for energy density at an applied current density of 50 mA cm -2 . An economic assessment indicated a levelized cost of storage at $410 per MWh under optimal conditions, highlighting the commercial potential of the Cu aq -TRAB when utilizing cost-effective, readily available materials.

25 ENERGY STORAGE↗
DOE OSTI2025

Efficient genetic code expansion tools enable in vivo study of lysine acetylation in non-model bacteria

Recent proteomic advancements have revealed widespread Nε-lysine acetylation in pathways governing pathogenicity, metabolism, and antibiotic resistance in bacteria. The spontaneous, non-specific nature of this modification in prokaryotes obscures its biological role, necessitating prokaryotic specific in vivo interrogation systems. Genetic Code Expansion (GCE) offers a powerful method to investigate the roles and regulation dynamics of acetyl-lysine in vivo with the precise incorporation of a suite of non-canonical amino acids, including acetyl-lysine analogs. However, its use has been largely restricted to E. coli strains due to challenges associated with implementation and optimization of the technology in more diverse bacterial strains. Here, we present a bacterial host-agnostic, readily optimizable GCE platform designed to site-specifically incorporate non-canonical amino acids into target proteins within living bacteria. We further demonstrate the versatility of this technology by showcasing, for the first time, the successful incorporation of acetyl-lysine in a non- E. coli bacterium.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

cis-p -Coumarates acylate the lignin sidechain in grasses and other plants

In this study, we present evidence that the lignins of grasses and other plants undergo partial acylation by cis-p-coumarate. Unlike the more widely observed trans-p-coumarates, cis-p -coumarates represent a novel acylation pattern on the lignin sidechains. The finding was substantiated by detailed NMR analyses (HSQC, HSQC-TOCSY, HMBC) and alkaline hydrolysis of the lignin isolated from abacá, a plant that exhibits substantial amounts of cis-p -coumarate. The presence of cis-p -coumarates broadens the range of groups known to acylate lignin sidechains and suggests that subtle variations in the acylation pattern can modulate the final structure and properties of the lignin. A broad survey of lignins from diverse plant species revealed that all lignins incorporating trans-p-coumarates also incorporated cis-p-coumarates, albeit in varying proportions. The cis-p-coumarate content ranged from 2 % to 12 % of the total p-coumarate units, depending on the plant species. As cis-p -coumarate is formed through the isomerization of trans-p-coumarate triggered by UV light, this transformation may occur at various stages, including at the free p-coumaric acid level, at the monolignol p-coumarate level, or directly within the lignin polymer. The potential pathways through which cis-p -coumaric acid becomes incorporated into the lignin are discussed.

NMR↗
DOE OSTI2022

Synthesis of the Candidate Topological Compound Ni 3 Pb 2

Spin-orbit coupling enables the realization of topologically nontrivial ground states. As spin-orbit coupling increases with increasing atomic number, compounds featuring heavy elements, such as lead, offer a pathway toward creating new topologically nontrivial materials. Here, by employing a high-pressure flux synthesis method, we synthesized single crystals of Ni 3 Pb 2 , the first structurally characterized bulk binary phase in the Ni-Pb system. Combining experimental and theoretical techniques, we examined structure and bonding in Ni 3 Pb 2 , revealing the impact of chemical substitutions on electronic structure features of importance for controlling topological behavior. From these results, we determined that Ni 3 Pb 2 completes a series of structurally related transition-metal-heavy main group intermetallic materials that exhibit diverse electronic structures, opening a platform for synthetically tunable topologically nontrivial materials.

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

Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics

Abstract The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism

Energy conservation in microorganisms is classically categorized into respiration and fermentation; however, recent work shows some species can use mixed or alternative bioenergetic strategies. We explored the use of extracellular electron transfer for energy conservation in diverse lactic acid bacteria (LAB), microorganisms that mainly rely on fermentative metabolism and are important in food fermentations. The LAB Lactiplantibacillus plantarum uses extracellular electron transfer to increase its NAD + /NADH ratio, generate more ATP through substrate-level phosphorylation, and accumulate biomass more rapidly. This novel, hybrid metabolism is dependent on a type-II NADH dehydrogenase (Ndh2) and conditionally requires a flavin-binding extracellular lipoprotein (PplA) under laboratory conditions. It confers increased fermentation product yield, metabolic flux, and environmental acidification in laboratory media and during kale juice fermentation. The discovery of a single pathway that simultaneously blends features of fermentation and respiration in a primarily fermentative microorganism expands our knowledge of energy conservation and provides immediate biotechnology applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Thirdhand cigarette smoke leads to age-dependent and persistent alterations in the cecal microbiome of mice

The gut microbiome composition is influenced by many factors including environmental exposures. Here, we investigated the effect of thirdhand cigarette smoke (THS) and exposure age on gut microbiome diversity. C57BL/6 mice were exposed to THS at human exposure relevant levels for three weeks during three different life stages: postnatal (0–3 weeks of age), pubescent (4–7 weeks of age), and adult (9–12 weeks of age), respectively. Cecal microbiome profiles were assessed at 17 weeks of age by 16S rRNA gene sequencing. We found that age at THS exposure strongly influenced the cecal microbiome composition. Although postnatal THS exposure significantly influenced the microbial composition, pubescent and adulthood exposures only had minor effects. The microbiome of postnatally THS-exposed mice significantly increased several degradation pathways that regulate glycolysis and pyruvate decarboxylation, and significantly decreased coenzyme A biosynthesis and pyrimidine deoxyribonucleoside salvage. Our results indicate that mouse postnatal development is particularly susceptible to persistent THS exposure effects on the gut microbiome.

16S rRNA gene sequencing↗
DOE OSTI2022

Itaconic acid production is regulated by LaeA in Aspergillus pseudoterreus

The global regulator LaeA controls secondary metabolism in diverse Aspergillus species. Here we explored its role in regulation of itaconic acid production in Aspergillus pseudoterreus. To understand its role in regulating metabolism, we deleted and overexpressed laeA, and assessed the transcriptome, proteome, and secreted metabolome prior to and during initiation of phosphate limitation induced itaconic acid production. We found that secondary metabolite clusters, including the itaconic acid biosynthetic gene cluster, are regulated by laeA and that laeA is required for high yield production of itaconic acid. Overexpression of laeA improves itaconic acid yield at the expense of biomass by increasing the expression of key biosynthetic pathway enzymes and attenuating the expression of genes involved in phosphate acquisition and scavenging. Increased yield was observed in optimized conditions as well as conditions containing excess nutrients that may be present in inexpensive sugar containing feedstocks such as excess phosphate or complex nutrient sources. This suggests that global regulators of metabolism may be useful targets for engineering metabolic flux that is robust to environmental heterogeneity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Pangenomes suggest ecological-evolutionary responses to experimental soil warming

ABSTRACT Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change. IMPORTANCE Anthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.

Choudoir, Mallory J. (ORCID:0000000291175150)↗
DOE OSTI2023

Ex vivo to in vivo model of malignant peripheral nerve sheath tumors for precision oncology

Malignant peripheral nerve sheath tumors (MPNST) are aggressive soft tissue sarcomas that often develop in patients with neurofibromatosis type 1 (NF1). To address the critical need for novel therapeutics in MPNST, we aimed to establish an ex vivo 3D platform that accurately captured the genomic diversity of MPNST and could be utilized in a medium-throughput manner for drug screening studies to be validated in vivo using patient-derived xenografts (PDX). Genomic analysis was performed on all PDX-tumor pairs. Selected PDX were harvested for assembly into 3D microtissues. Based on prior work in our labs, we evaluated drugs (trabectedin, olaparib, and mirdametinib) ex vivo and in vivo. For 3D microtissue studies, cell viability was the endpoint as assessed by Zeiss Axio Observer. For PDX drug studies, tumor volume was measured twice weekly. Bulk RNA sequencing was performed to identify pathways enriched in cells. We developed 13 NF1-associated MPNST-PDX and identified mutations or structural abnormalities in NF1 (100%), SUZ12 (85%), EED (15%), TP53 (15%), CDKN2A (85%), and chromosome 8 gain (77%). We successfully assembled PDX into 3D microtissues, categorized as robust (>90% viability at 48 h), good (>50%), or unusable (<50%). We evaluated drug response to “robust” or “good” microtissues, namely MN-2, JH-2-002, JH-2-079-c, and WU-225. Drug response ex vivo predicted drug response in vivo, and enhanced drug effects were observed in select models. These data support the successful establishment of a novel 3D platform for drug discovery and MPNST biology exploration in a system representative of the human condition.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Use-Inspired, Process-Oriented GCM Selection: Prioritizing Models for Regional Dynamical Downscaling

Dynamical downscaling is a crucial process for providing regional climate information for broad uses, using coarser-resolution global models to drive higher-resolution regional climate simulations. The pool of global climate models (GCMs) providing the fields needed for dynamical downscaling has increased from the previous generations of the Coupled Model Intercomparison Project (CMIP). However, with limited computational resources, the need for prioritizing the GCMs for subsequent downscaling studies remains. GCM selection for dynamical downscaling should focus on evaluating processes relevant for providing boundary conditions to the regional models and be inspired by regional uses such as the response of extremes to changes in the boundary conditions. This leads to the need for metrics representing processes of relevance to diverse stakeholders and subregions of a domain. Procedures to account for metric redundancy and the statistical distinguishability of GCM rankings are required. Further, procedures for selecting realizations from ensembles of top-performing GCM simulations can be used to span the range of climate change signals in multiple ways. As a result, distinct weighting of metrics and prioritization of particular realizations may depend on user needs. We provide high-level guidelines for such region-specific evaluations and address how CMIP7 might enable dynamical downscaling of a representative sample of high-quality models across representative shared socioeconomic pathways (SSPs).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The Role of Biofuels and Biomass Feedstocks for Decarbonizing the U.S. Economy by 2050 - (DECARB) Decarbonizing Energy Through Collaborative Analysis of Routes and Benefits

Utilizing biomass resources, such as cellulosic biomass and waste, can greatly contribute to decarbonization efforts in the U.S. economy. The U.S. bioenergy sector includes corn ethanol production, biodiesel, renewable diesel production, and the utilization of biomass wastes for electricity generation being the primary applications. Within the electricity sector, biopower can play a crucial role as a stable low-carbon resource. Enhancing the electricity mix's diversity could enhance grid reliability. If the issues regarding hot gas cleanup can be resolved, flexible biopower resources like biomass gasification facilities could complement the integration of variable renewable energy sources due to their quick ramp-up and ramp-down times. The criticality of bioenergy deployment lies in its ability to decarbonize hard-to-electrify sectors, such as aviation, where alternative decarbonization options may not be viable in the short term. Moreover, bioenergy has the potential to be converted into process heating, building materials, and plastics, which are not considered in this study. A set of pathways was carefully chosen to represent viable options for converting ample herbaceous and woody cellulosic feedstocks into fuels, chemicals, and electricity in this study. In conclusion, biomass pathways provide flexibility by generating various types of bioenergy and bioproducts, including electricity, hydrogen, liquid fuels, biochemicals, and bioplastics. When paired with carbon dioxide capture and storage (CCS), specific bioenergy approaches can effectively extract carbon dioxide from the atmosphere, thus providing an effective decarbonization option for the transportation sector.

09 BIOMASS FUELS↗
DOE OSTI2020

Intra‐species genetic variability drives carbon metabolism and symbiotic host interactions in the ectomycorrhizal fungus Pisolithus microcarpus

Summary Ectomycorrhizal (ECM) fungi are integral to boreal and temperate forest ecosystem functioning and nutrient cycling. ECM fungi, however, originate from diverse saprotrophic lineages and the impacts of genetic variation across species, and especially within a given ECM species, on function and interactions with the environment is not well understood. Here, we explore the extent of intra‐species variation between four isolates of the ECM fungus Pisolithus microcarpus , in terms of gene regulation, carbon metabolism and growth, and interactions with a host, Eucalyptus grandis . We demonstrate that, while a core response to the host is maintained by all of the isolates tested, they have distinct patterns of gene expression and carbon metabolism, resulting in the differential expression of isolate‐specific response pathways in the host plant. Together, these results highlight the importance of using a wider range of individuals within a species to understand the broader ecological roles of ECM fungi and their host interactions.

Plett, Krista L.↗
DOE OSTI2026

Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

Sorghum bicolor (Sorghum) is a drought and heat tolerant C4 grass crop used to produce grain, forage, biofuels, and other bioproducts. Genetic improvement of sorghum hybrid crops is aided by a large and diverse germplasm, sorghum's diploid inbreeding genetics, and a relatively small genome that has facilitated genomic research. Over the past 20 years, the sorghum research community characterized the cytogenetic and recombinant landscapes of sorghum's 10 chromosomes, sequenced and annotated the sorghum genome, and used that information to identify genes/alleles that modulate flowering time, plant height, seed shattering, and other important traits. More recently, >1000 RNA-seq transcriptome profiles were collected from 15 sorghum genotypes to help understand the genetic basis of variation in growth and development of sorghum stems, tillers, roots, and leaves, and the regulation of biosynthetic pathways that produce epicuticular wax, dhurrin, and RFOs, compounds that contribute to sorghum's resilience. Transcriptome studies were designed to identify differentially expressed genes that are co-expressed during development or in response to a treatment to enable construction of gene regulatory networks. Co-expression and network analysis identified transcription factors and their cognate binding sites in target gene promoters and signaling pathways that modulate gene regulatory networks providing gene editing targets for further trait optimization. RNA-seq data from >20 experiments targeting sorghum organs, tissues, cell types, developmental stages, and responses to environmental conditions (i.e., diel, day-length, shading, water-deficit, temperature) has been compiled in a sorghum transcriptome compendium. The goal of this resource paper is to describe compendium content, accessibility, and a compendium data analysis pipeline and to illustrate the types of information that can be derived from the compendium with a focus on the elucidation of gene regulatory networks useful for guiding the improvement of sorghum traits through gene editing.

RNA-seq↗
DOE OSTI2024

Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces

The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces .

59 BASIC BIOLOGICAL SCIENCES↗