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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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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Prenol production in a microbial host via the “Repass” Pathways

Prenol and isoprenol are promising advanced biofuels and serve as biosynthetic precursors for pharmaceuticals, fragrances, and other industrially relevant compounds. Despite engineering improvements that circumvent intermediate cytotoxicity and lower energy barriers, achieving high titer ‘mevalonate (MVA)-derived’ prenol has remained elusive. Difficulty in selective prenol production stems from the necessary isomerization of isopentenyl diphosphate (IPP) to dimethylallyl diphosphate (DMAPP) as well as the intrinsic toxicity of these diphosphate precursors. Here, the expression of specific isopentenyl monophosphate kinases with model-guided enzyme substitution of diphosphate isomerases and phosphatases enabled selective cycling of monophosphates and diphosphates, dramatically improving prenol titers and selectivity in Escherichia coli. Pairing this approach with the canonical MVA pathway resulted in 300 mg/L prenol at a 30:1 ratio with isoprenol. Further pairing with the “IPP-Bypass” pathway resulted in 526 mg/L prenol at a 72:1 ratio with isoprenol, the highest and purest MVA-derived prenol titer to date. Additionally, modifying this “IPP-Repass” for DMAPP production and coexpressing the prenyltransferase acPT1 yielded 48.3 mg/L of the potential therapeutic precursor drupanin from p-coumarate. These novel repass pathways establish a unique strategy for tuning diphosphate precursors to drive isoprenoid biosynthesis and prenylation reactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Host Onboarding Tool (HObT) v1.0.0

The Host OnBoarding Tool (Hobt) is a publicly accessible, web-based software designed to organize and share information about microbial hosts under development at the Agile BioFoundry (ABF). It streamlines the assessment, tracking, and sharing of information related to microbial host development and provides a centralized platform where users can rapidly evaluate hosts' readiness for various bio processes. HObT leverages the Tier System, a standardized host development framework that organizes and assesses microbial hosts based on their readiness for biomanufacturing. Each tier outlines key targets—including genetic tools, growth conditions, omics data, and predictive models—needed to transform new or emerging microbes into established production platforms. By applying clear criteria for advancement, the Tier System helps users quickly evaluate each organism's current development status, identify gaps in available knowledge or tools, and prioritize future strain improvement efforts. Through its user-friendly interface, HObT encourages contributions of new data and insights from researchers, fostering collaboration and accelerating host development. By providing structured guidance for microbial strain advancement, HObT and the Tier System support more systematic, rapid, and cost-effective development of non-traditional microbial hosts, ultimately enhancing the efficiency and impact of biomanufacturing research and applications.

Plahar, Hector [Lawrence Berkeley National Laborat↗
DOE OSTI2025

The tier system: a host development framework for bioengineering

Development of microorganisms into mature bioproduction host strains has typically been a slow and circuitous process, wherein multiple groups apply disparate approaches with minimal coordination over decades. To help organize and streamline host development efforts, we introduce the Tier System for Host Development, a conceptual model and guide for developing microbial hosts that can ultimately lead to a systematic, standardized, less expensive, and more rapid workflow. The Tier System is made up of three Tiers, each consisting of a unique set of strain development Targets, including experimental tools, strain properties, experimental information, and process models. By introducing the Tier System, we hope to improve host development activities through standardization and systematization pertaining to nontraditional chassis organisms.

09 BIOMASS FUELS↗
DOE OSTI2024

Development of Enzyme Production Host (CRADA Final Report)

This CRADA aims to assess the effectiveness of various enzyme production hosts in efficiently expressing and producing proprietary enzymes for plastic recycling applications. The research includes screening different microbial hosts—notably Bacillus subtilis, Pichia pastoris, and E. coli—to determine their suitability for high-yield enzyme production. Additionally, the project focuses on optimizing scalable fermentation processes tailored to these hosts, with the goal of enabling efficient enzyme production at commercially viable scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Development of Enzyme Production Host (CRADA Final Report)

This CRADA aims to assess the effectiveness of various enzyme production hosts in efficiently expressing and producing proprietary enzymes for plastic recycling applications. The research includes screening different microbial hosts—notably Bacillus subtilis, Pichia pastoris, and E. coli—to determine their suitability for high-yield enzyme production. Additionally, the project focuses on optimizing scalable fermentation processes tailored to these hosts, with the goal of enabling efficient enzyme production at commercially viable scales.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

A Catabolic Powerhouse for Biorefineries: Characterization and Engineering Erwinia spp. Strain LJJL01 to Produce Bioproducts

Nonmodel microbial hosts can efficiently biotransform unconventional organic feedstocks into advanced bioproducts, leveraging their superior metabolic capabilities and resilience to process-relevant physicochemical conditions. In this study, we domesticated Erwinia spp. strain. LJJL01 (Er LJJL01) as a potent microbial chassis to advance the emerging biorefinery strategy for the valorization of lignin-rich biomass and plastic, thereby enabling the circular economy. The strain exhibits remarkable chemical tolerance and can biofunnel various substrates, including sugars, acids, polyols, and aromatics, in minimal salt media to produce native fine chemicals such as acetoin, 2,3-butanediol, and lactic acid. As a proof of concept, engineering this strain with advanced genetic tools enables the production of tailored high-value chemicals, such as cis,cis-muconate from plastic-derived terephthalate and polyhydroxybutyrate from lignocellulosic hydrolysate. We established Er LJJL01 as a potent microbial chassis for the green synthesis of bioproducts from unconventional organic feedstocks.

09 BIOMASS FUELS↗
DOE OSTI2025

Microbiome dynamics in the congregate environment of U.S. Army Infantry training

Within military training and operational environments, individuals from diverse backgrounds share common spaces, follow structured routines and diets, and engage in physically demanding tasks. While there has been interest in leveraging microbiome features to predict and improve military health and performance, the longitudinal convergence of microbiomes in such constrained environments has not been established. To assess the degree of microbiome convergence, we performed shotgun metagenomic sequencing on swab samples from a military trainee cohort. Samples were taken across four different body sites, three timepoints, and two spatially distinct platoons. We observed evidence of convergence in one platoon, whereby similarity in microbiome composition increased over time, with numerous differentially abundant species. We found no indication of strain transfer between individuals, suggesting that convergence was influenced by external environmental factors, diet, and lifestyle. Microbial shifts observed in the convergence process included a decrease in fungal species, such as Malassezia restricta in nasal cavities, and a decrease in Prevotella species at inguinal regions across time. Shifts in multiple Corynebacterium species were also observed with varying magnitudes depending on the body site. Overall, we provide preliminary evidence of convergence of host microbial communities in military-associated environments that were distinguishable using shotgun metagenomic sequencing approaches. The data presented here on microbiome convergence, dynamics, and stability may inform risk-based mitigation in congregate military settings facilitating development of targeted microbial, dietary, or other interventions to optimize health and performance of military populations.

Biological and medical sciences↗
DOE OSTI2025

Microbial Pathways for Cost-Effective Low-Carbon Renewable Indigoidine

Indigoidine is a bioadvantaged platform molecule with diverse applications, including use as a textile dye, biotransistor, biosolar cell, biosensor, and food coloring. There are multiple microbial hosts and carbon sources that can be used and optimized for its production, yet there is limited guidance for which options have the greatest commercial potential. Here, we consider five different host microbes and combine genome-scale metabolic models with techno-economic and lifecycle assessment models. Pseudomonas putida currently outperforms synthetic indigo production and other indigoidine-producing hosts, using glucose, xylose, and lignin-derived aromatics to produce indigoidine at a minimum selling price of $2.9/kg and a greenhouse gas (GHG) footprint of 3.5 kgCO 2e /kg. Optimizing pathways-achieving 90% of the theoretical indigoidine yield from sugars and aromatics-can reduce costs 6-7-fold and GHG emissions 3-10-fold. From a cost perspective, microbes that co-utilize aromatics are advantageous, while selecting hosts that coproduce other value-added molecules can reduce GHG emissions. System-wide improvements and the use of a low-cost, low-carbon nitrogen source are crucial for commercial viability in all cases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Membrane Composition Influences Expression Yield of Plant Cytochrome P450s in E. coli Lysate-Based Cell-Free Systems

Plant cytochrome P450 enzymes are central to natural product biosynthesis, but remain difficult to express in microbial hosts due to their transmembrane nature. Lysate-based, cell-free expression systems allow supplementation with artificial membranes to support the expression and translocation of transmembrane proteins. We developed a framework to systematically test liposomal membrane compositions to enhance the plant P450 expression yield. Adjustments to common phospholipid ratios or the addition of plant galactolipids had minimal impact on expression. In contrast, blended liposomes containing Egg PC, sterol-conjugated phospholipids, and PEGylated lipids produced concentration-dependent increases in expression. Expression of an Escherichia coli mechanosensitive channel and three plant P450s improved more than 2-fold, with some P450s showing up to 14-fold enhancement. Furthermore, these findings highlight membrane composition as a key determinant of the P450 expression yield in cell-free expression systems. While P450 activity was not measured, these findings provide a framework for future workflows toward achieving functional plant transmembrane enzymes for the bioproduction of natural products.

TXTL↗
DOE OSTI2025

Oral microbiome and mycobiome dynamics in cancer therapy-induced oral mucositis

Cancer therapy-induced oral mucositis is a frequent major oncological problem, secondary to cytotoxicity of chemo-radiation treatment. Oral mucositis commonly occurs 7–10 days after initiation of therapy; it is a dose-limiting side effect causing significant pain, eating difficulty, need for parenteral nutrition and a rise of infections. The pathobiology derives from complex interactions between the epithelial component, inflammation, and the oral microbiome. Our longitudinal study analysed the dynamics of the oral microbiome (bacteria and fungi) in nineteen patients undergoing chemo-radiation therapy for oral and oropharyngeal squamous cell carcinoma as compared to healthy volunteers. The microbiome was characterized in multiple oral sample types using rRNA and ITS sequence amplicons and followed the treatment regimens. Microbial taxonomic diversity and relative abundance may be correlated with disease state, type of treatment and responses. Identification of microbial-host interactions could lead to further therapeutic interventions of mucositis to re-establish normal flora and promote patients’ health. Data presented here could enhance, complement and diversify other studies that link microbiomes to oral disease, prophylactics, treatments, and outcome.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Alternate routes to acetate tolerance lead to varied isoprenol production from mixed carbon sources in Pseudomonas putida

ABSTRACT Lignocellulose is a renewable resource for the production of a diverse array of platform chemicals, including the biofuel isoprenol. Although this carbon stream provides a rich source of sugars, other organic compounds, such as acetate, can be used by microbial hosts. Here, we examined the growth and isoprenol production in a Pseudomonas putida strain pre-tolerized (“PT”) background where its native isoprenol catabolism pathway is deleted, using glucose and acetate as carbon sources. We found that PT displays impaired growth in minimal medium containing acetate and often fails to grow in glucose-acetate medium. Using a mutant recovery-based approach, we generated tolerized strains that overcame these limitations, achieving fast growth and isoprenol production in the mixed carbon feed. Changes in the glucose and acetate assimilation routes, including an upregulation in PP_0154 (SpcC, succinyl-CoA:acetate CoA-transferase) and differential expression of the gluconate assimilation pathways, were key for higher isoprenol titers in the tolerized strains, whereas a different set of mechanisms were likely enabling tolerance phenotypes in media containing acetate. Among these, a coproporphyrinogen-III oxidase (HemN) was upregulated across all tolerized strains and in one isolate required for acetate tolerance. Utilizing a defined glucose and acetate mixture ratio reflective of lignocellulosic feedstocks for isoprenol production in P. putida allowed us to obtain insights into the dynamics and challenges unique to dual carbon source utilization that are obscured when studied separately. Together, this enabled the development of a P. putida bioconversion chassis able to use a more complex carbon stream to produce isoprenol. IMPORTANCE Acetate is a relatively abundant component of many lignocellulosic carbon streams and has the potential to be used together with sugars, especially in microbes with versatile catabolism such as P. putida . However, the use of mixed carbon streams necessitates additional optimization. Furthermore, the use of P. putida for the production of the biofuel target, isoprenol, requires the use of engineered strains that have additional growth and production constraints when cultivated in acetate and glucose mixtures. In this study, we generate acetate-tolerant P. putida strains that overcome these challenges and examine their ability to produce isoprenol. We show that acetate tolerance and isoprenol production, although independent phenotypes, can both be optimized in a given P. putida strain. Using proteomics and whole genome sequencing, we examine the molecular basis of both phenotypes and show that tolerance to acetate can occur via alternate routes and result in different impacts on isoprenol production.

de Siqueira, Guilherme M. V. (ORCID:00000002364563↗
DOE OSTI2025

Characterization of prokaryotic communities in Puerto Rican caves using 16S rDNA amplicon sequencing

The cave ecosystems host microbial communities adapted to extreme environments. This study utilized 16S rDNA to investigate the prokaryotic diversity across seven caves in Puerto Rico’s northern limestone karst belt. Microbial profiling revealed distinct subterranean communities, enhancing our understanding of cave microbiology and potential applications in environmental conservation and microbial research.

16S↗
DOE OSTI2025

Host Species–Microbiome Interactions Contribute to Sphagnum Moss Growth Acclimation to Warming

Sphagnum moss is the dominant plant genus in northern peatlands responsible for long-term carbon accumulation. Sphagnum hosts diverse microbial communities (microbiomes), and its phytobiome (plant host + constituent microbiome + environment) plays a key role in nutrient acquisition along with carbon cycling. Climate change can modify the Sphagnum -associated microbiome, resulting in enhanced host growth and thermal acclimation as previously shown in warming experiments. However, the extent of microbiome benefits to the host and the influence of host–microbe specificity on Sphagnum thermal acclimation remain unclear. Here, we extracted Sphagnum microbiomes from five donor species of four peatland warming experiments across a latitudinal gradient and applied those microbiomes to three germ-free Sphagnum species grown across a range of temperatures in the laboratory. Using this experimental system, we test if Sphagnum 's growth response to warming depends on the donor and/or recipient host species, and we determine how the microbiome's growth conditions in the field affect Sphagnum host growth across a range of temperatures in the laboratory. After 4 weeks, we found that the highest growth rate of recipient Sphagnum was observed in treatments of matched host–microbiome pairs, with rates approximately 50% and 250% higher in comparison to maximum growth rates of non-matched host–microbiome pairs and germ-free Sphagnum , respectively. We also found that the maximum growth rate of host–microbiome pairs was reached when treatment temperatures were close to the microbiome's native temperatures. Our study shows that Sphagnum's growth acclimation to temperature is partially controlled by its constituent microbiome. Strong Sphagnum host–microbiome species specificity indicates the existence of underlying, unknown physiological mechanisms that may drive Sphagnum 's ability to acclimatize to elevated temperatures. Together with rapid acclimation of the microbiome to warming, these specific microbiome–plant associations have the potential to enhance peatland resilience in the face of climate change.

acclimation↗
DOE OSTI2025

Digital Droplet PCR and Mesocosm-Based Methods to Evaluate Biocontainment Strategies in a Native Soil Ecosystem

Genetically modified industrial production microbes and their associated bioproducts have emerged as an integral component of a sustainable bioeconomy. However, the rapid development of these innovative technologies raises biosecurity concerns, namely, the risk of environmental escape. Thus, the realization of a bioeconomy hinges not only on the development and deployment of microbial production hosts, but also on the development of secure biosystems and biocontainment designs. Current laboratory-based biocontainment testing systems do not accurately reflect the complexities found in natural environments, necessitating an environmentally relevant analysis pipeline that allows for the detection of rare escapees within a complex soil microbiome and differentiation between closely related strains. To this end, we have developed an approach that utilizes soil mesocosms and integrated digital droplet PCR (ddPCR) system to evaluate the efficacy of novel biocontainment strategies. We demonstrate the utility of this approach by modeling contamination with industrial microbial chasses versus their biocontained counterparts. Here we demonstrate the broad utility of this system by highlighting findings from strains of Saccharomyces cerevisiae that are contained with an inducible toxin anti-toxin system, strains of Synechocystis sp. PCC 6803 contained via gene knockout or toxin anti-toxin system, and strains of Escherichia coli that are contained via genomic recoding. We also show that ddPCR can be used to detect gene copies from E. coli equal to those counted by traditional spot plating assays. The resultant data demonstrates that this system has broad utility across diverse microbial chassis and biocontainment strategies and enables researchers to track the fate of our contaminating microbe with high sensitivity in the soil. The findings presented here support the use of this mesocosm-based approach to assess the environmental impact of industrial microbes and to validate biocontainment strategies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

IMAGINE BioSecurity: Mesocosm-Based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native Ecosystems

Project Goals: The Integrative Modeling and Genome-scale Engineering for Biosystems Security (IMAGINE BioSecurity) SFA project seeks to establish an understanding of the behavior of engineered microbes in controlled versus environmental conditions to predictively devise new strategies for responding to biological escape. To this end, the IMAGINE Team has established a plant-soil mesocosm platform to track and quantify the fate of industrial microbes in environmental systems and assess the efficacy of biocontainment constraints upon genetically engineered microbe escape frequency and the impact of industrial microbes upon native ecological microbiomes. Abstract Text: Genetically modified industrial production microbes and their associated bioproducts have emerged as an integral component of a sustainable bioeconomy. However, the rapid development of these innovative technologies raises biosecurity concerns, namely, the risk of environmental escape. Thus, the realization of a bioeconomy hinges not only on the development and deployment of microbial production hosts, but also on the development of secure biosystems and biocontainment designs. Current laboratory-based biocontainment testing systems do not accurately reflect complexities found in natural environments, necessitating an environmentally relevant analysis pipeline that allows for the detection of rare escapees, the effect of associated bio-products, and the impact on native ecologies. To this end, we have developed an approach that utilizes soil mesocosms and integrated systems analyses to evaluate the efficacy of novel biocontainment strategies and to assess the impact of production systems upon terrestrial microbiome dynamics. We demonstrate the utility of this approach by modeling a contamination with industrial microbial chasses versus their biocontained counterparts. Here we demonstrate the broad utility of this system by highlighting findings from both strains of Saccharomyces cerevisiae that are contained with an inducible toxin anti-toxin system, and stains of Escherichia coli that are contained via genomic recoding. The resultant data demonstrate that this system has broad utility across diverse microbial chassis and biocontainment strategies, enables us to track the fate of our contaminating microbe with high sensitivity in the soil, as well as monitor broader impacts of the perturbation on the underlying soil system. The findings presented here support the use of this mesocosm-based approach to assess the environmental impact of industrial microbes and to validate biocontainment strategies.

BASIC BIOLOGICAL SCIENCES,INORGANIC, ORGANIC, PHYS↗
DOE OSTI2025

A small number of point mutations confer formate tolerance in Shewanella oneidensis

ABSTRACT Microbial electrosynthesis (MES) is a sustainable approach to chemical production from CO 2 and clean electricity. However, limitations in electron transfer efficiency and gaps in understanding of electron transfer pathways in MES systems prevent full realization of this technology. Shewanella oneidensis could serve as an MES biocatalyst because it has a well-studied, efficient transmembrane electron transfer pathway. A key first step in MES in this organism could be CO 2 reduction to formate. However, we report that wild-type S. oneidensis does not tolerate high levels of formate. In this work, we created and characterized formate-tolerant strains of S. oneidensis for further engineering and future use in MES systems through adaptive laboratory evolution. Two different point mutations in a gene encoding a predicted sodium-dependent bicarbonate transporter and a DUF2721-containing protein separately confer formate tolerance to S. oneidensis . The mutations were further evaluated to understand their role in improving formate tolerance. We also show that the wild-type and mutant versions of the putative sodium-dependent bicarbonate transporter improve formate tolerance of Zymomonas mobilis , indicating the potential of transferring this formate tolerance phenotype to other organisms. IMPORTANCE Shewanella oneidensis is a bacterium with a well-studied, efficient extracellular electron transfer pathway. This capability could make this organism a suitable host for microbial electrosynthesis using CO 2 or formate as feedstocks. However, we report here that formate is toxic to S. oneidensis , limiting the potential for its use in these systems. In this work, we evolve several strains of S. oneidensis that have improved formate tolerance, and we investigate some mutations that confer this phenotype. The phenotype is confirmed to be attributed to several single point mutations by transferring the wild-type and mutant versions of each gene to the wild-type strain. Finally, the formate tolerance mechanism of one variant is studied using structural modeling and expression in another host. This study, therefore, presents a simple method for conferring formate tolerance to bacterial hosts.

Cross, Megan C. Gruenberg (ORCID:0000000291589900)↗