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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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites

Secondary metabolites are not essential for the growth of microorganisms, but they play a critical role in how microbes interact with their surroundings. In addition to this important ecological role, secondary metabolites also have a variety of agricultural, medicinal, and industrial uses, and thus the examination of secondary metabolism of plants and microbes is a growing scientific field. While the chemical production of certain secondary metabolites is possible, industrial-scale microbial production is a green and economically attractive alternative. This is even more true, given the advances in bioengineering that allow us to alter the workings of microbes in order to increase their production of compounds of interest. This type of engineering requires detailed knowledge of the “chassis” organism’s metabolism. Since the resources and the catalytic capacity of enzymes in microbes is finite, it is important to examine the tradeoffs between various bioprocesses in an engineered system and alter its working in a manner that minimally perturbs the robustness of the system while allowing for the maximum production of a product of interest. The in silico multi-objective analysis of metabolism using genome-scale models is an ideal method for such examinations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities

In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting that multiple functional guilds feed on methane, likely through guild-to-guild carbon transfer, and potentially through intraguild and intraspecies interactions. We observed that, under two simulated dioxygen partial pressures—low versus high—community trajectories were different, with considerable variability among the replicates. In all microcosms, four major functional guilds were prominently present, representing Methylococcaceae (the true methanotrophs), Methylophilaceae (the nonmethanotrophic methylotrophs), Burkholderiales, and Bacteroidetes. Additional functional guilds were detected in multiple samples, such as members of Opitutae, as well as the predatory species, suggesting additional complexity for methane-oxidizing communities. Metatranscriptomic analysis suggested simultaneous expression of the two alternative types of methanol dehydrogenases in both Methylococcaceae and Methylophilaceae, while high expression of the oxidative/nitrosative stress response genes suggested competition for dioxygen among the community members. The transcriptomic analysis further suggested that Burkholderiales likely feed on acetate that is produced by Methylococcaceae under hypoxic conditions, while Bacteroidetes likely feed on biopolymers produced by both Methylococcaceae and Methylophilaceae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microbial Reduction of Geogenic and Synthetic Goethite and Hematite

The microbial reduction of Fe(III) is a major component of Fe cycling in terrestrial and aquatic environments and is affected by the Fe(III) mineralogy of the system. The majority of the research examining the bioreduction of Fe(III) oxides by Fe(III)-reducing bacteria (IRB) has focused on the reduction of poorly crystalline Fe(III) phases, primarily ferrihydrite; however, crystalline Fe(III) oxides like goethite (α-FeOOH) and hematite (α-Fe 2 O 3 ) comprise the majority of Fe(III) oxides in soils. This study examined the bioreduction of goethite and hematite of geogenic and synthetic origin by Shewanella putrefaciens CN2, a well-studied model IRB, in laboratory incubations. Overall, the rate and extent of Fe(II) production were greater for goethite than for hematite, and for geogenic Fe(III) oxides relative to their synthetic analogs. Although there was substantial production of Fe(II) (i.e., >5 mM Fe(II)) in many of the systems, X-ray diffraction analysis of the solids at the end of the incubation did not indicate the formation of any Fe(II)-bearing secondary minerals (e.g., magnetite, siderite, green rust, etc.). The results of this study demonstrate the variability in the extent of bioreduction of geogenic goethite and hematite, and furthermore, that synthetic goethite and hematite may not be good analogs for the biogeochemical behavior of Fe(III) oxides in aquatic and terrestrial environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mercury Methylation and Soil Organic Matter Degradation in Incubations with Added Acetate, Isotope-Labeled Mercury, and Selective Microbial Inhibitors, Teller and Council Sites, Seward Peninsula, 2018-2019

This dataset provides the results of laboratory soil microcosm incubation experiments conducted under anaerobic conditions with added acetate, isotope-labeled mercury, and selective microbial inhibitors (2-bromoethanesulfonate and sodium molybdate). The microcosms contained soil collected in August 2018 from the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) near Intensive Site 9 (TL_IS_9) and from the Council Road Site (CN_MM71). Incubations were conducted at 8°C for 180 days (Teller incubations) or 60 days (Council incubations). The microcosm headspace was sampled at designated intervals for greenhouse gas concentrations, then destructively harvested and extracted using ultrapure water and 0.1 M KCl for analysis of the porewater geochemistry. This dataset contains one pdf, two csv data files, and one zipped file with raw data.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in a Biological Nutrient Removal Plant Operated at Hamptons Road Sanitation District (HRSD) with High and Low Dissolved Oxygen Conditions

In this study, we aimed to evaluate Biological Nutrient Removal (BNR) and investigate microbial community changes as the dissolved oxygen is reduced in the aerated portions of wastewater treatment trains. We present a dataset of Metagenome-Assembled Genomes (MAGs) obtained from activated sludge collected from the Hamptons Road Sanitation District (HRSD) BNR plant at the beginning of operation, when the DO was high, and at the end of operation, when the DO was low.

Genomics↗
DOE OSTI2025

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in a Biological Nutrient Removal Plant Operated at Los Angeles County Sanitation District (LACSD) with High and Low Dissolved Oxygen Conditions

In this study, we aimed to evaluate Biological Nutrient Removal (BNR) and investigate microbial community changes as the dissolved oxygen is reduced in the aerated portions of wastewater treatment trains. We present a dataset of Metagenome-Assembled Genomes (MAGs) obtained from activated sludge collected from the Los Angeles County Sanitation District (LACSD) BNR plant at the beginning of operation, when the DO was high, and at the end of operation, when the DO was low.

Genomics↗
DOE OSTI2020

Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme

The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Δ 1 -pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.

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

How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population’s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population’s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Project Methods to Enhance Wellbore Cement Integrity with Microbially-Induced Calcite Precipitation (MICP) (Final Scientific/Technical Report)

The goal of this project was to develop improved methods for sealing compromised wellbore cement in leaking oil and gas wells, thereby reducing the risk of unwanted upward fluid migration. Novel methods for improving wellbore integrity, such as microbially induced calcite precipitation (MICP), can reduce leakage potential, improve the safety of fossil fuel extraction, improve the public perception of hydraulic fracturing, and promote environmentally-prudent unconventional oil and gas development. Microbes, with the urease enzyme, can catalyze the chemical reaction of urea hydrolysis to induce the precipitation of calcium carbonate which can be used as a cementitious material to seal leakage pathways. In this project, methods to promote robust bio-composite cementitious materials were designed and tested in the laboratory. Scale-up of those methods were tested in meso-scale reactor systems and in field applications. In this report, in Section One, we describe laboratory efforts to develop injection strategies to promote precipitation in wellbore analogs and determine the strength of the bio-composite cements as compared to fine cement. In Section Two, we describe the efforts to scale up the work and study the use of materials that can be used in field application, for example exploring the use of calcium chloride ice melt or urea fertilizer as source chemicals. In Section Three, the three field trials (methods and results) performed as part of the project are described and summarized. At the end of the report is a comprehensive summary and conclusion section which highlights the key findings of the project. The work performed during this project significantly advanced the technology readiness level (TRL) of the MICP wellbore sealing strategy.

02 PETROLEUM↗
DOE OSTI2020

Methods to Enhance Wellbore Cement Integrity with Microbially-Induced Calcite Precipitation (MICP) (Final Scientific/ Technical Report)

The goal of this project was to develop improved methods for sealing compromised wellbore cement in leaking oil and gas wells, thereby reducing the risk of unwanted upward fluid migration. Novel methods for improving wellbore integrity, such as microbially induced calcite precipitation (MICP), can reduce leakage potential, improve the safety of fossil fuel extraction, improve the public perception of hydraulic fracturing, and promote environmentally-prudent unconventional oil and gas development. Microbes, with the urease enzyme, can catalyze the chemical reaction of urea hydrolysis to induce the precipitation of calcium carbonate which can be used as a cementitious material to seal leakage pathways. In this project, methods to promote robust bio-composite cementitious materials were designed and tested in the laboratory. Scale-up of those methods were tested in meso-scale reactor systems and in field applications. In this report, in Section One, we describe laboratory efforts to develop injection strategies to promote precipitation in wellbore analogs and determine the strength of the bio-composite cements as compared to fine cement. In Section Two, we describe the efforts to scale up the work and study the use of materials that can be used in field application, for example exploring the use of calcium chloride ice melt or urea fertilizer as source chemicals. In Section Three, the three field trials (methods and results) performed as part of the project are described and summarized. At the end of the report is a comprehensive summary and conclusion section which highlights the key findings of the project. The work performed during this project significantly advanced the technology readiness level (TRL) of the MICP wellbore sealing strategy.

03 NATURAL GAS↗
DOE OSTI2021

Automated microbial detection and quantification

A method for automated microbial detection includes collecting air particles into a solid-state sampler, the air particles including microbes, charging the air particles using a plasma field generated by propulsion electrodes, focusing the charged air particles toward a sample well of a microfluidic testing cartridge, tagging the charged air particles with a fluorescence marker, and detecting a quantity of the microbes using a fluorescence detector.

Gilbert, James H.↗
DOE OSTI2021

Microbial syringol utilization

Disclosed herein are compositions of non-naturally occurring enzymes to enable microbial syringol utilization with GcoAB.

Beckham, Gregg Tyler↗
DOE OSTI2020

Microbial potentiometric sensor array measurements in unsaturated soils

The overarching goal of this study is to demonstrate a novel technology for monitoring changes in electrical potential of unsaturated soils using biofilm-populated electrodes. The novelty of the study stems from the fact that it demonstrates a method for measuring open-circuit potentials (OCP) in environments without the presence of an electrolyte solution. This study also reveals that using a biofilm-populated electrode as a reference in stable environments could successfully be employed to assess and monitor the electrochemical potential generated by plants and microorganisms. The findings imply that long-term (months to years) and real-time measurements of the open-circuit potential in unsaturated soils are possible. Because MPS arrays can directly measure open-circuit potential from the biofilm, the challenges related to locally induced electrochemical changes caused by microorganisms in the soil to achieve optimum physiological levels are eliminated. The simplicity of the technology, which allows for multiple indicator electrodes to be referenced against an “internal” reference electrode, enables spatial-temporal monitoring of the changes in the soil and the generation of 2D- or 3D-signal patterns. Once a signal pattern, generated by an array of sensors, develops (usually after 30 to 90 days), it does not significantly change unless the soil is exposed to external stimuli. The observed OCP phenomena, however, suggests that the change in OCP signal is independent of changes in soil conductivity resulting from the addition of water. In brief, findings suggest that the proposed technology can enable multidimensional profiling and long-term monitoring of changes occurring in unsaturated soils without direct implications of presence of water. The changes in the 2D or 3-D signal patterns, however, can be correlated to other important parameters that characterize soil health.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Toward FAIR Representations of Microbial Interactions

Despite an ever-growing number of data sets that catalog and characterize interactions between microbes in different environments and conditions, many of these data are neither easily accessible nor intercompatible. These limitations present a major challenge to microbiome research by hindering the streamlined drawing of inferences across studies.

59 BASIC BIOLOGICAL SCIENCES↗