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At least 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Methods and systems of characterizing and counting microbiological colonies

Described herein are methods, systems, and non-transitory computer-readable media to non-destructively acquire three-dimensional profiles of cellular microbiological samples growing on the surface of a solid growth medium. Acquisitions can be performed by an optical microscope that includes a vertical scanning interferometer. The three-dimensional profiles can enable measurement of sample parameters of microcolonies, which can be made of microbial colony forming units. The methods and systems enable early and rapid detection and quantification of microbes.

Larimer, Curtis J.↗
DOE OSTI2022

Devices and methods for generating electrical current from methane

Methods, microbial fuel cells and microbial consortia for generating electrical current are provided according to the present invention which include providing a microbial consortium to an anode chamber of a microbial fuel cell, wherein the microbial consortium includes: 1) an engineered methanogen that contains a heterologous nucleic acid sequence encoding methyl-coenzyme M reductase derived from an anaerobic methane oxidizer, 2) an exoelectrogen microbe that produces electrically-conductive appendages and/or one or more types of electron carrier, and 3) a sludge, methane-acclimated sludge, a sludge isolate component, a methane-acclimated sludge isolate component chosen from Paracoccus spp., Geotoga spp., Geobacter spp., Methanosarcina spp., Garciella spp., humic acids; or a combination of any two or more thereof.

Wood, Thomas K.↗
DOE OSTI2023

Gas-Liquid Flow Modeling for Renewable Fuels Production

Aerobic/anaerobic and gas fermentation pathways have emerged as promising new technologies for the generation of renewable fuels/chemicals from biomass derived sugars, and mixtures of greenhouse/energy rich gas streams (CO2/CH4/H2/CO) via microbial action. Example pathways include sugars-to-ethanol conversion, biomethanation (CO2/H2 to CH4), biogas upgrading, CO fermentation and wet-waste conversion. Gas and liquid phase transport, mass-transfer, and mixing physics at large length scales can significantly affect microbial conversion rates, particularly when the microbial reaction requires a narrow set of conditions. These phenomena are difficult to study in small-scale bench-top reactors that are typically well-mixed. Predictive computational fluid dynamics (CFD) based simulations can therefore aid in the scale-up, design and optimization of these reactors. This work presents multiphase Euler-Euler CFD simulations of at-scale (~500 m3) bioreactors. Our mathematical model treats the gas and liquid as interpenetrating phases. This approach reduces the computational complexity of tracking individual gas bubbles that are several orders of magnitude smaller than reactor dimensions. We solve the Reynolds averaged Navier-Stokes (RANS) multiphase equations that account for phase and chemical species transport, interphase mass and momentum transfer and uses a phenomenological model for gas uptake by microbes. We use a customized solver derived from open-source CFD toolbox, OpenFOAM [1], to perform these simulations, which has been validated against small-scale reactors in our previous work [2]. There is currently a knowledge-gap regarding bubble-size distributions when using gas mixtures with vastly different properties, which can have a significant impact overall mass-transfer. For example, hydrogen bubbles are more buoyant compared to other relatively heavier gases (CO2/CH4/CO), resulting in a large distribution of residence times and bubble sizes. This work therefore develops a deeper understanding of bubble dynamics and interphase mass transfer in such heterogenous gas mixtures through well-resolved computational models. We use a population balance model (PBM) for bubble-size-distribution modeling that is validated against small-scale experiments in our solver with an uncertainty quantification study for bubble coalescence and break-up model parameters. Results pertaining to multiple simulations of gas-fermentation reactors are presented where gas mixtures with varying compositions of CO2/CH4/CO/H2 are imposed at the sparger boundaries. The spatio-temporal variations in bubble-size distribution and mass transfer coefficient are analyzed for varying superficial velocities and gas-compositions for varying sizes of bubble-column and airlift reactors. This work will also examine the performance of different reactor designs, viz. bubble column reactor, airlift reactor with an internal draft tube, and a stirred-tank reactor with Rushton impellers. Reactor mass-transfer coefficient, gas hold-up, and dissolved gas distribution are critically analyzed among reactors, and sensitivity studies pertaining to gas flow rates and reactor geometry will be presented. [1] Weller, H., Tabor, G., Jasak, H. and Fureby, C., A tensorial approach to computational continuum mechanics using object-oriented techniques, Computers in physics, 12, 6, 620--631, 1998. [2] Rahimi, M., Sitaraman, H., Humbird, D. and Stickel, J., Computational fluid dynamics study of full-scale aerobic bioreactors: Evaluation of gas-liquid mass transfer, oxygen uptake, and dynamic oxygen distribution, Chemical Engineering Research and Design, 139: 283-295.

BIOMASS FUELS↗
DOE OSTI2024

Quantifying microbial roles in environmental iron oxidation via an integrated kinetics, `omics and metabolic modeling study (Final Report)

Iron oxyhydroxides are extremely reactive components of environmental systems, and therefore exert a strong influence on biogeochemical cycles. These oxyhydroxides strongly adsorb many biologically-relevant elements, including organic carbon and phosphate, as well as a wide range of metals including uranium and actinide species. Thus, the formation mechanism of iron oxyhydroxides are key to understanding both nutrient and contaminant cycling. Microorganisms can catalyze iron oxidation and promote the formation of Fe biominerals and thus are increasingly recognized as important players in biogeochemical cycling. However, it is completely unknown how much of environmental iron oxidation is biologically mediated versus abiotic, and various challenges in studying microbial iron oxidation have hindered accurate incorporation into hydrobiogeochemical models. The overarching goal of our work was to quantify and constrain microbial iron oxidation rates and use ‘omics to gain insight into the controls on this process, while developing tools to enable integration of biotic iron oxidation into hydrobiogeochemical models. Our work focused on the Savannah River Site (SRS) in South Carolina, where extensive microbial iron oxidation has been observed. At Tims Branch, part of the Argonne National Laboratory Wetland Hydrobiogeochemistry Science Focus Area (Argonne SFA), where groundwater discharges into a stream, iron-oxidizing microbial mats form and appear to be a major sink of uranium. In the wetlands that surround Tims Branch, there are wide swaths of iron microbial mats and flocs (mobilized mat). We measured biotic and abiotic iron oxidation rates using mats and water sampled from these sites and found that iron oxidation is primarily carried out by chemolithotrophic microorganisms. The resulting rate constants can be incorporated into models. These mats were characterized by metagenomics and metatranscriptomics, which showed that aerobic chemolithotrophs were the dominant iron-oxidizing bacteria (FeOB), and these included Gallionellaceae and Leptothrix, and possibly Rhodoferax, which is known as an Fe-reducer but may also oxidize Fe(II). This demonstrated that diverse FeOB can coexist and suggests that there are a range of niches and therefore drivers of chemolithotrophic iron oxidation. Analysis of reconstructed genomes strongly suggests that a major factor in diversity is carbon source, as genomes contained varied pathways for autotrophy and heterotrophy. We performed an in-depth analysis of Leptothrix ochracea genomes, since this sheath-former is one of the primary mat builders, yet its physiology remained unresolved. A combination of genomics, transcriptomics, and metabolic modeling suggest that L. ochracea grows mixotrophically using a combination of Fe(II) and organics for energy and both inorganic and organic carbon to create biomass. This contrasts with the largely autotrophic Gallionellaceae (Gallionella, Sideroxydans, and Ferriphaselus) also present in the mats and flocs. Remarkably, multiple FeOB, both Leptothrix and Gallionellaceae, showed activity in response to Fe(II) in live mat incubations. We tracked the gene expression of individual MAGs to Fe(II) and found that various autotrophic and heterotrophic FeOB responded to Fe(II), increasing expression of both carbon fixation and organic utilization genes. The results of the integrated field, kinetics, and omics studies give detailed insight into 1) the taxa that oxidize Fe, and 2) how they connect Fe, C, and N cycles. Towards the goal of connecting omics data to hydrobiogeochemical models, we worked with the KBase team to create a template metabolic model for chemolithotrophic iron oxidation. We initially modeled the well-characterized isolate Gallionellaceae Sideroxydans lithotrophicus, and also applied the model to the mixotroph L. ochracea. In all, we have characterized diverse FeOB in a representative wetland system and solved key problems that enable better incorporation of iron-oxidizing microbes into hydrobiogeochemical models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Electromethanogenesis reactor

Generation of energy and storage of energy for subsequent use is provided by electromethanogenesis of carbon dioxide into a fuel gas and the storage of the fuel gas for subsequent use. An electromethanogenic reactor includes an anode conductor and a cathode conductor wherein the cathode conductor includes submicron to micron scale pores. Electromethanogenesis microbes and/or enzymes are located in the micron scale pores of the cathode electrode conductor. Carbon dioxide is introduced into the electromethanogenic reactor and the electromethanogenesis microbes/enzymes and the carbon dioxide interact and produce a fuel gas. The fuel gas is stored for subsequent use, for example use in power generation.

Knipe, Jennifer Marie↗
DOE OSTI2025

Development of Biological and Electrochemical Technologies for the Clean Extraction of Copper and Critical Materials from Low Grade Ores

As we transition toward renewable energy resources and electrification, there will be an increasing demand for critical materials, including copper. While copper is currently mined in the US, processing capacity is not sufficient, and intermediate mining products are shipped to Asia for further processing. The goal of this research was to develop a transformative hydrometallurgical process for the production of copper from low-grade ores that would eliminate the need for smelting and would increase the domestic processing capacity in the US, The project initially focused on the electrochemical reduction of copper concentrate using vanadium, followed by the biological oxidation to produce a stream compatible with existing solvent extraction and electrowinning operations. We discovered an efficient electrochemical process that could produce copper salts from concentrate without the need for biological oxidation, and this technology has been licensed and spun-off into a start-up company. The microbes involved in the current state-of-the-art bioleaching processes were genetically modified to introduced a number of new traits, including increased sulfur oxidation, salt-tolerance, and binding of other critical metals such as cobalt, molybdenum, rhenium, and the rare earth elements. The project was extended to also explore the electrochemical oxidation of copper concentrate using cerium which would potentially eliminate production of hydrogen sulfide that occurs with the reductive leaching process. This technology was found to have slower kinetics, however could it still be developed as an alternative process for domestic copper production and has been found to be applicable to other critical minerals.

42 ENGINEERING↗
DOE OSTI2026

Production of Renewable Solvents and Monomers from Lignocellulosic Feedstocks

Lignocellulosic biomass is pretreated and broken down into cellulosic sugars. The cellulosic sugars are converted to mevalonolactone (MVL) using Visolis’ proprietary microbes. The MVL containing broth is separated from the cells, deashed-decolorized, concentrated and fed into a catalytic reactor to develop anhydro mevalonolactone (aMVL), and 3-methyl pentanediol (3MPD). The products were separated by distillation into high purity compounds as solvent or polymer applications.

3-methyl pentanediol, polymer, solvent↗
DOE OSTI2025

Impact of Storage Conditions on the Quality and Viability of Switchgrass as a Bioenergy Crop

With growing energy demands and climate concerns, advancements in bioenergy have become imperative. Biofuels promote energy independence, reduce fossil fuel reliance, and cut greenhouse gas emissions. Switchgrass (Panicum virgatumis) is an ideal bioenergy crop due to its ability to thrive on marginal lands unsuitable for food crops and its drought tolerance, rendering it a low-maintenance, high-yield option. In the bioenergy industry, energy crops are typically stored to facilitate supply chain management and ensure a continuous supply despite seasonal availability. However, the effective utilization of bioenergy crops is typically contingent upon addressing the challenges associated with biomass storage. These challenges include high moisture content that promotes biological degradation of the biomass leading to increased risk of pathogenic microbes, and chemical degradation that increases the ratio of inconvertible, inorganic materials. These issues lead to a reduction of feedstock value, diminishing the biomass-to-biofuel conversion efficacy, making switchgrass and other bioenergy crops less effective as fuel sources. This project aims to improve the storage of purpose-grown energy crops. Aerobic storage trials were conducted under varying moisture contents to stimulate real-world environmental exposure. Switchgrass samples were rewetted to 30% or 35% and stored in a bioreactor for approximately one month, or until cellular respiration ceased. Degradation indicators, such as dry matter loss, temperature changes, and cellular respiration, were measured throughout this process. Samples for compositional analysis, 16S, and ITS were taken at three different time points: before, during, and after storage, to monitor changes in biomass, microbial communities, and metabolites over time. Preliminary data indicate that dry matter loss is proportional to cellular respiration, with higher moisture content (35%) leading to higher temperatures and elevated dry matter loss. Compositional analysis and microbial community analysis are in progress. This research will provide a comprehensive understanding of storage, helping to identify stability factors in energy crops and improve best management practices for biomass producers.

09 - BIOMASS FUELS↗
DOE OSTI2021

Structure of the Extracellular Region of the Bacterial Type VIIb Secretion System Subunit EsaA

Gram-positive bacteria use type VII secretion systems (T7SSs) to export effector proteins that manipulate the physiology of nearby prokaryotic and eukaryotic cells. Several mycobacterial T7SSs have established roles in virulence. By contrast, the genetically distinct T7SSb pathway found in Firmicutes bacteria more often functions to mediate bacterial competition. A lack of structural information on the T7SSb has limited the understanding of effector export by this protein secretion apparatus. Here, we present the 2.4 angstrom crystal structure of the extracellular region of the T7SSb subunit EsaA from Streptococcus gallolyticus. Our structure reveals that homodimeric EsaA is an elongated, arrow-shaped protein with a surface-accessible "tip", which in some species of bacteria serves as a receptor for lytic bacteriophages. Because it is the only T7SSb subunit large enough to traverse the peptidoglycan layer of Firmicutes, we propose that EsaA plays a critical role in transporting effectors across the entirety of the Gram-positive cell envelope.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Root carbon interation with soil minerals is dynamic, leaving a legacy of microbially derived residues

Minerals preserve the oldest most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that carbon source and soil microorganisms also influence mineral-SOM associations, we incubated permeable minerals bags in soil microcosms with and without plants, in a 13CO2 labelling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or native soil minerals isolated via density separation. Using 13C-NMR, FTICR-MS, and lipidomics, we traced plant-derived carbon onto minerals harvested from microcosms at three plant growth stages, characterizing total carbon, 13C enrichment, and SOM chemistry. While C accumulation was rapid and mineral-dependent, the accumulated amount was not significantly affected by the presence of plant roots. However, the rhizosphere did shape the chemistry of mineral-associated SOM. Minerals incubated in the rhizosphere were associated with a more diverse array of compounds with different C functional groups (carbonyl, aromatics, carbohydrates, lipids) than minerals incubated in a bulk soil control. These diverse rhizosphere-derived compounds may represent a “transient fraction” of mineral SOM, rapidly exchanging with mineral surfaces. Our results also suggest that many of the lipids which persist on minerals are microbially-derived with a large fraction of fungal lipids.

Rhizosphere, soil organic matter, grassland, 13C-N↗
DOE OSTI2025

Dissolved Organic Carbon in Coastal Waters: Global Patterns, Stocks and Environmental Physical Controls

Abstract Dissolved organic carbon (DOC) in coastal waters is integral to biogeochemical cycling, but global and regional drivers of DOC are still uncertain. In this study we explored spatial and temporal differences in DOC concentrations and stocks across the global coastal ocean, and how these relate to temperature and salinity. We estimated a global median coastal DOC stock of 3.15 Pg C (interquartile range (IQR) = 0.85 Pg C), with median DOC concentrations being 2.2 times higher than in open ocean surface waters. Globally and seasonally, salinity was the main driver of DOC with concentrations correlated negatively with salinity, without a clear relationship to temperature. DOC concentrations and stocks varied with region and season and this pattern is likely driven by riverine inputs of DOC and nutrients that stimulate coastal phytoplankton production. Temporally, high DOC concentrations occurred mainly in months with high freshwater input, with some exceptions such as in Eastern Boundary Current margins where peaks are related to primary production stimulated by nutrients upwelled from the adjacent ocean. No spatial trend between DOC and temperature was apparent, but many regions (19 out of 25) had aligned peaks of seasonal temperature and DOC, related to increased phytoplankton production and vertical stratification at high temperatures. Links of coastal DOC with salinity and temperature highlight the potential for anthropogenic impacts to alter coastal DOC concentration and composition, and thereby ecosystem status.

Lønborg, Christian [Section for Marine Diversity a↗
DOE OSTI2024

Dynamic nitrogen fixation in an aerobic endophyte of Populus

Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte–poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15 N 2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant–endophyte interactions.

15 N-tracking metabolomics↗