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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms

Growth rate has long been considered one of the most valuable phenotypes that can be measured in cells. Aside from being highly accessible and informative in laboratory cultures, maximal growth rate is often a prime determinant of cellular fitness, and predicting phenotypes that underlie fitness is key to both understanding and manipulating life. Despite this, current methods for predicting microbial fitness typically focus on yields [e.g., predictions of biomass yield using GEnomescale metabolic Models (GEMs)] or notably require many empirical kinetic constants or substrate uptake rates, which render these methods ineffective in cases where fitness derives most directly from growth rate. Here we present a new method for predicting cellular growth rate, termed SUMEX, which does not require any empirical variables apart from a metabolic network (i.e., a GEM) and the growth medium. SUMEX is calculated by maximizing the SUM of molar EXchange fluxes (hence SUMEX) in a genome-scale metabolic model. SUMEX successfully predicts relative microbial growth rates across species, environments, and genetic conditions, outperforming traditional cellular objectives (most notably, the convention assuming biomass maximization). The success of SUMEX suggests that the ability of a cell to catabolize substrates and produce a strong proton gradient enables fast cell growth. Easily applicable heuristics for predicting growth rate, such as what we demonstrate with SUMEX, may contribute to numerous medical and biotechnological goals, ranging from the engineering of faster-growing industrial strains, modeling of mixed ecological communities, and the inhibition of cancer growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Microorganisms Associated with Hydrocarbon Contaminated Sites and Reservoirs for Microbially Enhanced Oil Recovery (MEOR)

Russian partner Institutes tested a number of strains from their collection and/or selected at oilfield contamination/ extraction sites to determine their ability to create aggregates that could plug oil well reservoirs to enhance oil recovey. Among these tested, five facultative anaerobic organisms that performed the best in the Russian Institutes' trials were shipped to Argonne and evaluated at Argonne for their ability to produce aggregates that plug pores in oil reservoirs formations. Results were provided to the Industrial Partner who is interested in receiving the strains for further testing.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2012

Systems-Level Description of Metabolic and Regulatory Pathways for a Hydrogen-Producing Model Microorganism

We sought to improve our understanding of the metabolic and regulatory networks that control hydrogen (H 2 ) production in the hyperthermophilic marine archaeon Pyrococcus furiosus (Pf), a model microbial H 2 producer. We used an approach based on genomic and transcriptomic analyses of stress response along with genetic and biochemical characterization of identified pathways to further define control checkpoints in H 2 production that will be valuable in future metabolic engineering efforts.

Scott, Robert↗
DOE OSTI2015

The effects of Fe-oxidizing microorganisms on post-biostimulation permeability reduction and oxidative processes at the Rifle IFRC site

Fe oxidation and biomineral formation is important in aquifers because the highly-reactive oxides can control the mobility of nutrients (e.g. phosphate, C) and metals (e.g. arsenic, uranium). Mineral formation also has the potential to affect hydrology, depending on the volume and distribution in pore spaces. In this exploratory study, we sought to understand how microbial Fe-oxidizers and their biominerals affect, and are affected by groundwater flow. As part of work at the Rifle aquifer in Colorado, we initially hypothesized that Fe-oxidizers were contributing to aquifer clogging problems associated with enhanced bioremediation. To demonstrate the presence of Fe-oxidizers in the Rifle aquifer, we enriched FeOM from groundwater samples, and isolated two novel chemolithotrophic, microaerophilic Fe-oxidizing Betaproteobacteria, Hydrogenophaga sp. P101 and Curvibacter sp. CD03. To image cells and biominerals in the context of pores, we developed a “micro-aquifer,” a sand-filled flow-through culture chamber that allows for imaging of sediment pore space with multiphoton confocal microscopy. Fe oxide biofilms formed on sand grains, demonstrating that FeOM produce Fe oxide sand coatings. Fe coatings are common on aquifer sands, and tend to sequester contaminants; however, it has never previously been shown that microbes are responsible for their formation. In contrast to our original hypothesis, the biominerals did not clog the mini-aquifer. Instead, Fe biofilm distribution was dynamic: they grew as coatings, then periodically sloughed off sand grains, with some flocs later caught in pore throats. This has implications for physical hydrology, including pore scale architecture, and element transport. The sloughing of coatings likely prevents the biominerals from clogging wells and aquifers, at least initially. Although attached biomineral coatings sequester Fe-associated elements (e.g. P, As, C, U), when biominerals detach, these elements are transported as particles through the aquifer. Our work shows that microbial mineralization impacts in aquifers are dynamic, and that the fate and transport of biomineral-associated elements depend not only on geochemical conditions, but also physical pore-scale processes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Investigations into the metabolic diversity of microorganisms as part of microbial diversity

DOE funds supported a key portion of the MBL Microbial Diversity (Woods Hole) program across 6 complete summers. The initial 4 years of the funded period were overseen by two co-Directors, Daniel Buckley (Cornell) and Steve Zinder (Cornell), who then completed their term. The final 2 summers were overseen by 2 new co-Directors, Jared R. Leadbetter (Caltech) and Dianne Newman (Caltech). The 6 funded summer iterations of the course included the incorporation of new themes such as single cell approaches applied to natural microbial communities (cell separation and sorting, genome amplification from single cells, and the use of Nano-SIMS to examine assimilation of carbon and nitrogen from isotopically labeled substrates into single cells), genetics and genomics on bacteria freshly isolated during the course of the programs, quantitative systems biology, and modern quantitative light microscopy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Synthetic Design of Microorganisms for Lignin Fuel

Despite the proof-of-the-concept for lignin bioconversion at the time when the project was first funded, the conversion efficiency and titer were extremely low for bioconversion of lignin into lipid. The low conversion efficiency is due the inherent recalcitrance of lignin and limited understanding of lignin chemistry. In nature, lignin is a complex aromatic heteropolymer composed of phenylpropane units cross-linked via a variety of chemically stable bonds, which makes it particularly difficult for microbial degradation. In addition to the recalcitrance, lignin as a biorefinery waste is also highly heterogeneous in terms of chemical linkage abundance, functional group distribution, molecular weight and uniformity. In order to achieve better lignin bioconversion, it is critical to understand how lignin chemistry impacts the conversion performance. Throughout the project, we have clearly found that ‘not all lignin are created equal’, in particular, for the lignin out of different biochemical conversion processes. In addition, we have clearly shown that lignin chemistry defines its functionality and processiblity for bioconversion. In particular, the S/G/H ratio, functional groups, chemical linkages and molecular weight defines the reactivity of lignin during bioconversion. Throughout the project, we have advanced the understanding for the impact of lignin chemistry on reactivity, developed a series of lignin 3 fractionation technologies to improve lignin processibility, and ultimately advanced biorefinery design holistically for simultaneous optimization of carbohydrate release and lignin reactivity. In addition to lignin reactivity, another important consideration for lignin bioconversion is the available microbial strains for bioconversion. Natural biomass utilization systems evolved mechanisms for lignin degradation, often with at least three sequential steps: lignin depolymerization into aromatic compounds, subsequent degradation of aromatic compounds into common intermediates like acetyl-CoA, and eventually the conversion of central metabolites into target bioproducts like lipid and PHA. Extensive work has gone into understanding the mechanisms of lignin depolymerization in model systems such as white rot fungi and termites. Despite interest, no fungus-based commercial process for lignin depolymerization has been developed, due in large part to the practical challenges of fungal genetic manipulations. In addition to white rot fungi, a few members of the Actinobacteria, α-Proteobacteria, and γ-Proteobacteria (including Rhodococcus putida) have lignin degradation activity in vitro. However, most of lignindegrading bacteria has very low lignin conversion efficiency, in particular, for lignin depolymerization. The project focused on addressing the issue with systems biology-guided microbial design to improve lignin bioconversion. The project first established that laccase enzyme can synergize with bacteria to promote lignin depolymerization, and further utilized synthetic biology approach to designed functional modules for lignin depolymerization, aromatic compound utilization, and bioproduct accumulation. The integration of biorefinery design, synthetic biology, and fermentation optimization eventually allowed us to achieve the target yield of 10g/L lipid production from lignin-containing biorefinery waste. In this summary, we hereby briefly review the major discoveries from the project with reference to different sections of this report.

09 BIOMASS FUELS↗
DOE OSTI2024

Engineered Microorganisms for Enhanced Rare Earth Element Bio-mining and Separations (Final Technical Report)

Rare earth elements (REE) are critical ingredients of sustainable energy technologies, but their extraction from ore and separation from one another pose formidable challenges. To solve the challenge of REE supply, we used advanced genomics, high-throughput screening with synthetic REE minerals, and synthetic biology to engineer two sets of exotic microbes to (1) extract REE from ores, spent cracking catalysts, coal ash and electronic waste with high efficiency and selectivity, and (2) to purify REE into single element batches, all under benign conditions without the need of harsh solvents and high temperatures. This work integrated our expertise in systems and synthetic biology (Buz Barstow); rare-earth geochemistry (Esteban Gazel) and mineral synthesis (Megan Holycross); and microsystems engineering (Mingming Wu) by first elucidating the set of rules that predict an organism’s phenotype and then applying them to solve this critical problem in sustainable energy. These new technologies could help to revitalize the US rare earth industry and provide a new source of these critical elements for future energy technologies. We have already had some big success in tech transfer. Two of our team members (postdoctoral fellow Alexa Schmitz and graduate student Sean Medin) were able to study the supply chain for REE in the United States, and identify an opportunity to commercialize our REE mineral-dissolution technology. Alexa and Sean recently founded REEgen, Inc., an REE biomining company. Dr. Schmitz was recently awarded a fellowship from the Activate Foundation to support the first two years of REEgen. Cornell showed its support for this technology and company, and Dr. Schmitz was awarded the Rising Women Innovator’s award. These two awards unlocked support from Cornell’s Praxis Incubator.

58 GEOSCIENCES↗
DOE OSTI2012

Microbial Iron Cycling in Acidic Geothermal Springs of Yellowstone National Park: Integrating Molecular Surveys, Geochemical Processes, and Isolation of Novel Fe-Active Microorganisms

Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats inYellowstone National Park. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 88°C and pH 2.4 to 3.6. All iron oxide mats exhibited high diversity of crenarchaeal sequences from the Sulfolobales, Thermoproteales, and Desulfurococcales. The predominant Sulfolobales sequences were highly similar to Metallosphaera yellowstonensis str. MK1, previously isolated from one of these sites. Other groups of archaea were consistently associated with different types of iron oxide mats, including undescribed members of the phyla Thaumarchaeota and Euryarchaeota. Bacterial sequences were dominated by relatives of Hydrogenobaculum spp. above 65–70°C, but increased in diversity below 60°C. Cultivation of relevant iron-oxidizing and iron-reducing microbial isolates included Sulfolobus str. MK3, Sulfobacillus str. MK2, Acidicaldus str. MK6, and a new candidate genus in the Sulfolobales referred to as Sulfolobales str. MK5. Strains MK3 and MK5 are capable of oxidizing ferrous iron autotrophically, while strain MK2 oxidizes iron mixotrophically. Similar rates of iron oxidation were measured for M. yellowstonensis str. MK1 and Sulfolobales str. MK5. Biomineralized phases of ferric iron varied among cultures and field sites, and included ferric oxyhydroxides, K-jarosite, goethite, hematite, and scorodite depending on geochemical conditions. Strains MK5 and MK6 are capable of reducing ferric iron under anaerobic conditions with complex carbon sources. The combination of geochemical and molecular data as well as physiological observations of isolates suggests that the community structure of acidic Fe mats is linked with Fe cycling across temperatures ranging from 53 to 88°C.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H2) transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H2 was metabolized into CH4 by methanogens. Collectively, our results demonstrate the importance of inter-species interactions for the biomass-degrading and methane-producing phenotype of the rumen microbiome—both microbially facilitated processes with global significance.

interspecies H2 transfer↗
DOE OSTI2021

Diversifying Isoprenoid Platforms via Atypical Carbon Substrates and Non-model Microorganisms

Isoprenoid compounds are biologically ubiquitous, and their characteristic modularity has afforded products ranging from pharmaceuticals to biofuels. Isoprenoid production has been largely successful in Escherichia coli and Saccharomyces cerevisiae with metabolic engineering of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways coupled with the expression of heterologous terpene synthases. Yet conventional microbial chassis pose several major obstacles to successful commercialization including the affordability of sugar substrates at scale, precursor flux limitations, and intermediate feedback-inhibition. Now, recent studies have challenged typical isoprenoid paradigms by expanding the boundaries of terpene biosynthesis and using non-model organisms including those capable of metabolizing atypical C1 substrates. Conversely, investigations of non-model organisms have historically informed optimization in conventional microbes by tuning heterologous gene expression. Here, we review advances in isoprenoid biosynthesis with specific focus on the synergy between model and non-model organisms that may elevate the commercial viability of isoprenoid platforms by addressing the dichotomy between high titer production and inexpensive substrates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Editorial: Microorganisms for Consolidated 2nd Generation Biorefining

In the last few decades, lignocellulosic biomass has attracted substantial interest as a feedstock for fermentative production of fuels and other commodity chemicals due to its wide availability and low cost. However, lignocellulose has innate complexity and recalcitrance to biodegradation. In natural environments, effective plant biomass decay is obtained by synergistic activity of complex microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant

Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g −1 , which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant ( p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria，Sordariomycetes and Dothideomycetes . Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.

Shen, Qihui↗
DOE OSTI2020

A Rapid and High Throughput MIC Determination Method to Screen Uranium Resistant Microorganisms

The assessment of minimum inhibitory concentration (MIC) is a conventional technique used for the screening of microbial resistance against antibiotics, biocides, and contaminants such as heavy metals. However, as part of our ongoing work, we have observed biases associated with using traditional liquid MIC method to screen microbial heavy metal resistance, including both bacterial and fungal strains. Specifically, the addition of uranium into synthetic media causes immediate precipitation prior to the initiation of microbial growth, thus hampering the optical density measurements, and the obtained MIC values are thus flawed and inaccurate. To address this discrepancy, we report the optimization and development of a serial-dilution-based MIC method conducted on solid growth media supplemented with uranium, which is more accurate, relative to the testing of MICs performed in liquid cultures. Notably, we report on the efficacy of this method to screen not only bacteria that are resistant to uranium but also demonstrate the successful application to yeast and fungal isolates, for their ability to resist uranium, is more accurate and sensitive relative to the liquid method. We believe that this newly developed method to screen heavy metal resistance, such as uranium, is far superior to the existing liquid MIC method and propose replacing the liquid assay with the solid plate MIC reported herein.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil’s opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.

59 BASIC BIOLOGICAL SCIENCES↗