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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

BETO 2021 Peer Review - Improving Formate Upgrading by Cupriavidus Necator 2.3.2.111

Formate can be generated by electrocatalytic reduction of CO2 and has been proposed as a soluble intermediate for the storage of carbon and energy. Biological systems capable of assimilating formate could enable conversion of formate generated from low-cost renewable energy and waste CO2 to myriad fuels and chemicals. To that end, the goal of this project is to develop the natural formatotroph Cupriavidus necator as a robust microbial chassis for efficient conversion of formate to value-added products. Using a combination of laboratory evolution and rational engineering, we have identified mutations and genetic deletions that improve its growth rate and biomass yield on formate by 1.2X. Using RNA-seq transcriptomics, we are elucidating the mechanisms that underly these improvements and anticipate this will contribute to our understanding of formate conversion. We have also engineered C. necator to convert formate to the potential polymer precursor 2-hydroxymuconate semialdehyde (2HMS) by introducing an exogenous pathway and deleting competing pathways and demonstrated production and robust growth using a pH-stat bioreactor. Final techno-economic analysis and life-cycle assessment on biological production of 2HMS from formate will enable the DOE and other stake holders to evaluate the economic and environmental impact of this project and related technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2019

Microbial Biomarker Transition in High-Altitude Sinter Mounds From El Tatio (Chile) Through Different Stages of Hydrothermal Activity

Geothermal springs support microbial communities at elevated temperatures in an ecosystem with high preservation potential that makes them interesting analogs for early evolution of the biogeosphere. The El Tatio geysers field in the Atacama Desert has astrobiological relevance due to the unique occurrence of geothermal features with steep hydrothermal gradients in an otherwise high altitude, hyper-arid environment. We present here results of our multidisciplinary field and molecular study of biogeochemical evidence for habitability and preservation in silica sinter at El Tatio. We sampled three morphologically similar geyser mounds characterized by differences in water activity (i.e., episodic liquid water, steam, and inactive geyser lacking hydrothermal activity). Multiple approaches were employed to determine (past and present) biological signatures and dominant metabolism. Lipid biomarkers indicated relative abundance of thermophiles (dicarboxylic acids) and sulfate reducing bacteria (branched carboxylic acids) in the sinter collected from the liquid water mound; photosynthetic microorganisms such as cyanobacteria (alkanes and isoprenoids) in the steam sinter mound; and archaea (squalane and crocetane) as well as purple sulfur bacteria (cyclopropyl acids) in the dry sinter from the inactive geyser. The three sinter structures preserved biosignatures representative of primary (thermophilic) and secondary (including endoliths and environmental contaminants) microbial communities. Sequencing of environmental 16S rRNA genes and immuno-assays generally corroborated the lipid-based microbial identification. The multiplex immunoassays and the compound-specific isotopic analysis of carboxylic acids, alkanols, and alkanes indicated that the principal microbial pathway for carbon fixation in the three sinter mounds was through the Calvin cycle, with a relative larger contribution of the reductive acetyl-CoA pathway in the dry system. Other inferred metabolic traits varied from the liquid mound (iron and sulfur chemistry), to the steam mound (nitrogen cycle), to the dry mound (perchlorate reduction). The combined results revealed different stages of colonization that reflect differences in the lifetime of the mounds, where primary communities dominated the biosignatures preserved in sinters from the still active geysers (liquid and steam mounds), in contrast to the surviving metabolisms and microbial communities at the end of lifetime of the inactive geothermal mound.

Lipid biomarkers, geothermal springs, sinter, biog↗
DOE OSTI2025

Editorial: Ecology, evolution, and biodiversity of microbiomes and viromes from extreme environments

Ecology, evolution, and biodiversity of microbiomes and viromes in extreme environments are key areas of research that explore how microbial communities adapt, survive, and thrive under harsh conditions. The studies published in our Research Topic advance our understanding of microbial and viral diversity, evolutionary processes, and the ecological roles of these communities, with implications for biotechnology, climate resilience, and even astrobiology.

adaptation↗
DOE OSTI2021

Cellular remains in a ~3.42-billion-year-old subseafloor hydrothermal environment

Subsurface habitats on Earth host an extensive extant biosphere and likely provided one of Earth’s earliest microbial habitats. Though the site of life’s emergence continues to be debated, evidence of early life provides insights into its early evolution1. Here we present our discovery of exceptionally well-preserved ~3.40-billion-years-old carbonaceous filamentous microfossils that inhabited a paleo-subseafloor hydrothermal vein system of the Barberton greenstone belt (BGB) in South Africa. The distribution of the microfossils in growth position on the walls of the initial conduits created by low- temperature hydrothermal fluid and their morphological and chemical characteristics as investigated over a range of scales, are consistent with an assemblage of methanogens that thrived in an ultramafic volcanic substrate.

Cavalazzi, Barbara↗
DOE OSTI2024

From wolves to humans: oral microbiome resistance to transfer across mammalian hosts

The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria

Taking a look at plant-microbe relationships Ever since plants colonized land, they have evolved a range of mutualistic associations with bacteria and fungi. Indeed, such associations were probably required for plants to grow on harsh, nutrient-poor surfaces. Martin et al. review the spectrum of plant-microbe symbioses and their evolution, including evidence from the Rhynie Chert of the Devonian period and modern associations. Surprisingly, diverse functional plant-microbial symbioses have several common conserved features, including signaling pathways, immune evasion, and root development. Science , this issue p. eaad4501

Martin, Francis M.↗
DOE OSTI2024

Adaptive laboratory evolution and genetic engineering improved terephthalate utilization in Pseudomonas putida KT2440

Poly(ethylene terephthalate) (PET) is one of the most ubiquitous plastics and can be depolymerized through biological and chemo-catalytic routes to its constituent monomers, terephthalic acid (TPA) and ethylene glycol (EG). TPA and EG can be re-synthesized into PET for closed-loop recycling or microbially converted into higher-value products for open-loop recycling. Here, in this study, we expand on our previous efforts engineering and applying Pseudomonas putida KT2440 for PET conversion by employing adaptive laboratory evolution (ALE) to improve TPA catabolism. Three P. putida strains with varying degrees of metabolic engineering for EG catabolism underwent an automation-enabled ALE campaign on TPA, a TPA and EG mixture, and glucose as a control. ALE increased the growth rate on TPA and TPA-EG mixtures by 4.1- and 3.5-fold, respectively, in approximately 350 generations. Evolved isolates were collected at the midpoints and endpoints of 39 independent ALE experiments, and growth rates were increased by 0.15 and 0.20 h -1 on TPA and a TPA-EG, respectively, in the best performing isolates. Whole-genome re-sequencing identified multiple converged mutations, including loss-of-function mutations to global regulators gacS, gacA, and turA along with large duplication and intergenic deletion events that impacted the heterologously-expressed tphAB II catabolic genes. Reverse engineering of these targets confirmed causality, and a strain with all three regulators deleted and second copies of tphAB II and tpaK displayed improved TPA utilization compared to the base strain. Taken together, an iterative strain engineering process involving heterologous pathway engineering, ALE, whole genome sequencing, and genome editing identified five genetic interventions that improve P. putida growth on TPA, aimed at developing enhanced whole-cell biocatalysts for PET upcycling.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Electrons to Molecules by Engineering and Evolution: Biological Upgrading of Formate by Cupriavidus necator

Waste carbon from industrial point sources can be captured, stored, and/or transformed using electrochemical conversion or "electrons to molecules" technologies using low-cost renewable electricity. One such process involves electrocatalytic reduction of CO2 to generate formate/formic acid, a C1 carboxylic acid. Formate is a promising potential feedstock for microbial upgrading, as it is water soluble and can be consumed as the sole source of carbon and energy by some microbial species, such as the soil bacterium Cupriavidus necator. Here we will present progress toward improving C. necator as a host for biological conversion of formate to value-added products. Using the power of adaptive laboratory evolution, we were able to isolate mutants of C. necator with significantly faster growth rates on formate. We then sequenced the genomes of these strains, elucidated the metabolic role of the mutations we found, and then used these insights to build rationally engineered strains that outperform even the best evolved isolates. These results highlight the utility of "genome streamlining" as a route for generating platform strains with potential industrial applications.

adaptive laboratory evolution↗
DOE OSTI2017

Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution

There is a need to replace petroleum-derived with sustainable feedstocks for chemical production. Certain biomass feedstocks can meet this need as abundant, diverse, and renewable resources. Specific ionic liquids (ILs) can play a role in this process as promising candidates for chemical pretreatment and deconstruction of plant-based biomass feedstocks as they efficiently release carbohydrates which can be fermented. However, the most efficient pretreatment ILs are highly toxic to biological systems, such as microbial fermentations, and hinder subsequent bioprocessing of fermentative sugars obtained from IL-treated biomass. To generate strains capable of tolerating residual ILs present in treated feedstocks, a tolerance adaptive laboratory evolution (TALE) approach was developed and utilized to improve growth of two different Escherichia coli strains, DH1 and K-12 MG1655, in the presence of two different ionic liquids, 1-ethyl-3-methylimidazolium acetate ([C 2 C 1 Im][OAc] ) and 1-butyl-3-methylimidazolium chloride ([C 4 C 1 Im]Cl). For multiple parallel replicate populations of E. coli , cells were repeatedly passed to select for improved fitness over the course of approximately 40 days. Clonal isolates were screened and the best performing isolates were subjected to whole genome sequencing. The most prevalent mutations in tolerant clones occurred in transport processes related to the functions of mdtJI , a multidrug efflux pump, and yhdP , an uncharacterized transporter. Additional mutations were enriched in processes such as transcriptional regulation and nucleotide biosynthesis. Finally, the best-performing strains were compared to previously characterized tolerant strains and showed superior performance in tolerance of different IL and media combinations (i.e., cross tolerance) with robust growth at 8.5% (w/v) and detectable growth up to 11.9% (w/v) [C 2 C 1 Im][OAc]. The generated strains thus represent the best performing platform strains available for bioproduction utilizing IL-treated renewable substrates, and the TALE method was highly successful in overcoming the general issue of substrate toxicity and has great promise for use in tolerance engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Electrocatalytic Hydrogen Evolution in Neutral pH Solutions: Dual-Phase Synergy

Electrolysis in neutral pH solutions (e.g., wastewater and seawater) presents a transformative way for environmentally friendly, cost-effective hydrogen production. However, one of the biggest challenges is the lack of active, robust hydrogen evolution reaction (HER) catalysts. Herein we present a catalyst with dual active sites of MoP2 and MoP which function synergistically to promote HER in neutral pH solutions. In our microbial electrolysis cell (MEC) which uses neutral pH wastewater as a feedstock, the new catalyst generates an average HER current density of ~157 A m-2Cathode-Surface-Area, higher than Pt/C (~145 A m-2Cathode-Surface-Area), ~5 times higher than the state-of-art platinum-group-metal (PGM)-free catalysts in MECs. The new catalyst also outperforms Pt/C in natural seawater with ~10% higher and more stable HER current density. The fundamental reason for the enhanced HER performance is identified to be the synergy between MoP2 and MoP phases, with MoP2 promoting H2O chemisorption/dissociation and MoP efficiently converting Hads to H2.

Xie, Xiaohong↗
DOE OSTI2019

Robust and biocompatible catalysts for efficient hydrogen-driven microbial electrosynthesis

Abstract CO 2 reduction by combined electro- and bio-catalytic reactions is a promising technology platform for sustainable production of chemicals from CO 2 and electricity. While heterogeneous electrocatalysts can reduce CO 2 to a variety of organic compounds at relatively high reaction rates, these catalysts have limitations achieving high selectivity for any single product beyond CO. Conversely, microbial CO 2 reduction pathways proceed at high selectivity; however, the rates at bio-cathodes using direct electron supply via electricity are commonly limiting. Here we demonstrate the use of non-precious metal cathodes that produce hydrogen in situ to support microbial CO 2 reduction to C 1 and C 2 compounds. CoP, MoS 2 and NiMo cathodes perform durable hydrogen evolution under biologically relevant conditions, and the integrated system achieves coulombic efficiencies close to 100% without accumulating hydrogen. Moreover, the one-reactor hybrid platform is successfully used for efficient acetate production from electricity and CO 2 by microbes previously reported to be inactive in bioelectrochemical systems.

Kracke, Frauke (ORCID:0000000261253162)↗
DOE OSTI2020

Single-Cell Genomics and the Oral Microbiome

The human oral cavity is one of the first environments where microbes have been discovered and studied since the dawn of microbiology. Nevertheless, approximately 200 types of bacteria from the oral microbiota have remained uncultured in the laboratory. Some are associated with a healthy oral microbial community, while others are linked to oral diseases, from dental caries to gum disease. Single-cell genomics has enabled inferences on the physiology, virulence, and evolution of such uncultured microorganisms and has further enabled isolation and cultivation of several novel oral bacteria, including the discovery of novel interspecies interactions. This review summarizes some of the more recent advances in this field, which is rapidly moving toward physiologic characterization of single cells and ultimately cultivation of the yet uncultured. A combination of traditional microbiological approaches with genomic-based physiologic predictions and isolation strategies may lead to the oral microbiome being the first complex microbial community to have all its members cultivable in the laboratory. We conclude studying the biology of the individual microbes when in association with other members of the community, in controlled laboratory conditions and in vivo, should lead to a better understanding of oral dysbiosis and its prevention and reversion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Application of functional genomics for domestication of novel non-model microbes

Abstract With the expansion of domesticated microbes producing biomaterials and chemicals to support a growing circular bioeconomy, the variety of waste and sustainable substrates that can support microbial growth and production will also continue to expand. The diversity of these microbes also requires a range of compatible genetic tools to engineer improved robustness and economic viability. As we still do not fully understand the function of many genes in even highly studied model microbes, engineering improved microbial performance requires introducing genome-scale genetic modifications followed by screening or selecting mutants that enhance growth under prohibitive conditions encountered during production. These approaches include adaptive laboratory evolution, random or directed mutagenesis, transposon-mediated gene disruption, or CRISPR interference (CRISPRi). Although any of these approaches may be applicable for identifying engineering targets, here we focus on using CRISPRi to reduce the time required to engineer more robust microbes for industrial applications. One-Sentence Summary The development of genome scale CRISPR-based libraries in new microbes enables discovery of genetic factors linked to desired traits for engineering more robust microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Tropical Forest Soil Microbiome Modulates Leaf Heat Tolerance More Strongly Under Warming Than Ambient Conditions

ABSTRACT It is unclear how plants respond to increasing temperatures. Leaf heat tolerance (LHT) is often at its upper limit in tropical forests, suggesting that climate change might negatively impact these forests. We hypothesized that intraspecific variation in LHT might be associated with changes in the soil microbiome, which might also respond to climate. We hypothesized that warming would increase LHT through changes in the soil microbiome: we combined an in situ tropical warming experiment with a shade house experiment in Puerto Rico. The shade house experiment consisted of growing seedlings of Guarea guidonia , a dominant forest species, under different soil microbiome treatments (reduced arbuscular mycorrhizal fungi, reduced plant pathogens, reduced microbes, and unaltered) and soil inoculum from the field experiment. Heat tolerance was determined using chlorophyll fluorescence ( F V /F m ) on individual seedlings in the field and on groups of seedlings (per pot) in the shade house. We sequenced soil fungal DNA to analyze the impacts of the treatments on the soil microbiome. In the field, seedlings from ambient temperature plots showed higher F V /F m values under high temperatures (0.648 at 46°C and 0.067 at 52°C) than seedlings from the warming plots (0.535 at 46°C and 0.031 at 52°C). In the shade house, the soil microbiome treatments significantly influenced the fungal community composition and LHT ( T crit and F V /F m ). Reduction in fungal pathogen abundance and diversity altered F V /F m before T 50 for seedlings grown with soil inoculum from the warming plots but after T 50 for seedlings grown with soil inoculum from the ambient plots. Our findings emphasize that the soil microbiome plays an important role in modulating the impacts of climate change on plants. Understanding and harnessing this relationship might be vital for mitigating the effects of warming on forests, emphasizing the need for further research on microbial responses to climate change.

Hernandes Villani, Gabriela [Department of Plant B↗
DOE OSTI2020

Hydrogen production from lignocellulosic hydrolysate in an up-scaled microbial electrolysis cell with stacked bio-electrodes

Hydrogen production from renewable resources via microbial electrolysis cells (MECs) is a promising approach for sustainable energy production. Yet high hydrogen yield from real feedstocks has not been demonstrated in up-scaled MECs. In this study, a 10-L single chamber MEC with a high electrode surface area to volume ratio (66 m 2 /m 3 ) was constructed and electroactive cathodic biofilms were enriched for hydrogen evolution reaction. A high hydrogen yield of 91% was achieved using lignocellulosic hydrolysate with a hydrogen production rate of 0.71 L/L/D at an organic loading rate of 0.4 g/D. The anodic and cathodic microbial communities, with Enterococcus spp. as the known electroactive bacteria, were capable of achieving current densities of 13.7 A/m 2 and 16.5 A/m 2 , respectively. Finally, a machine learning algorithm was used to investigate the correlation between community data and electrochemical performance, and the critical genera on determining current density were identified.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community

The recalcitrance of complex organic polymers such as lignocellulose is one of the major obstacles to sustainable energy production from plant biomass, and the generation of toxic intermediates can negatively impact the efficiency of microbial lignocellulose degradation. Here, we describe the development of a model microbial consortium for studying lignocellulose degradation, with the specific goal of mitigating the production of the toxin formaldehyde during the breakdown of methoxylated aromatic compounds. Included are Pseudomonas putida, a lignin degrader; Cellulomonas fimi, a cellulose degrader; and sometimes Yarrowia lipolytica, an oleaginous yeast. Unique to our system is the inclusion of Methylorubrum extorquens, a methylotroph capable of using formaldehyde for growth. We developed a defined minimal “Model Lignocellulose” growth medium for reproducible coculture experiments. We demonstrated that the formaldehyde produced by P. putida growing on vanillic acid can exceed the minimum inhibitory concentration for C. fimi, and, furthermore, that the presence of M. extorquens lowers those concentrations. We also uncovered unexpected ecological dynamics, including resource competition, and interspecies differences in growth requirements and toxin sensitivities. Finally, we introduced the possibility for a mutualistic interaction between C. fimi and M. extorquens through metabolite exchange. This study lays the foundation to enable future work incorporating metabolomic analysis and modeling, genetic engineering, and laboratory evolution, on a model system that is appropriate both for fundamental eco-evolutionary studies and for the optimization of efficiency and yield in microbially-mediated biomass transformation.

Methylorubrum extorquens↗
DOE OSTI2021

In vivo evolution of lactic acid hyper-tolerant Clostridium thermocellum

Lactic acid (LA) has several applications in the food, cosmetics and pharmaceutical industries, as well as in the production of biodegradable plastic polymers, namely polylactides. Industrial production of LA is essentially based on microbial fermentation. Recent reports have shown the potential of the cellulolytic bacterium Clostridium thermocellum for direct LA production from inexpensive lignocellulosic biomass. However, C. thermocellum is highly sensitive to acids and does not grow at pH < 6.0. Improvement of LA tolerance of this microorganism is pivotal for its application in cost-efficient production of LA. In the present study, the LA tolerance of C. thermocellum strains LL345 (wild-type fermentation profile) and LL1111 (high LA yield) was increased by adaptive laboratory evolution. At large inoculum size (10 %), the maximum tolerated LA concentration of strain LL1111 was more than doubled, from 15 g/L to 35 g/L, while subcultures evolved from LL345 showed 50–85 % faster growth in medium containing 45 g/L LA. Gene mutations (pyruvate phosphate dikinase, histidine protein kinase/phosphorylase) possibly affecting carbohydrate and/or phosphate metabolism have been detected in most LA-adapted populations. Although improvement of LA tolerance may sometimes also enable higher LA production in microorganisms, C. thermocellum LA-adapted cultures showed a yield of LA, and generally of other organic acids, similar to or lower than parental strains. Based on its improved LA tolerance and LA titer similar to its parent strain (LL1111), mixed adapted culture LL1630 showed the highest performing phenotype and could serve as a framework for improving LA production by further metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Transplanting the pathway engineering toolbox to methanogens

Biological methanogenesis evolved early in Earth’s history and was likely already a major process by 3.5 Ga. Modern methanogenesis is now a key process in virtually all anaerobic microbial communities, such as marine and lake sediments, wetland and rice soils, and human and cattle digestive tracts. Owing to their long evolution and extensive adaptations to various habitats, methanogens possess enormous metabolic and physiological diversity. Not only does this diversity offers unique opportunities for biotechnology applications, but also reveals their direct impact on the environment, agriculture, and human and animal health. These efforts are facilitated by an advanced genetic toolbox, emerging new molecular tools, and systems-level modelling for methanogens. Further developments and convergence of these technical advancements provide new opportunities for bioengineering methanogens.

59 BASIC BIOLOGICAL SCIENCES↗