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DOE OSTI2020

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

The soil microbiome is an invaluable component of the biosphere and critical for ecosystem functions, including biogeochemical cycling, soil-atmosphere gas exchange, degradation of toxic compounds, and promotion of plant growth and stress resistance/resilience. An improved understanding of the soil microbiome will help with predicting how these processes respond to external perturbations, and with harnessing beneficial aspects of the soil microbiome for agronomic applications such as crop amendments. However, the extensive taxonomic and functional diversity inherent within the soil microbiome hinders efficient analysis of this system. Microbial biodiversity in soils is orders of magnitude greater than other commonly studied systems such as the human gut microbiome (Blum, Zechmeister-Boltenstern, and Keiblinger 2019; Berendsen, Pieterse, and Bakker 2012). Thousands of microbial taxa may be found in a single gram of soil (Roesch et al. 2007), and high rates of gene flow and mutation further promote microbial diversification (Sergaki et al. 2018). Concomitantly, functional diversity in soil is similarly extensive. Soil is a heterogeneous mixture of microenvironments with defined physical and chemical attributes (Bach et al. 2018), within which numerous microbial guilds of distinct life-strategies and metabolic capacities can be found (Perez-Garcia, Lear, and Singhal 2016; H.-S. Song et al. 2014). Furthermore, the soil microbiome harbors a significant fraction of rare and/or quiescent members (Blagodatskaya and Kuzyakov 2013) that exist below the threshold of detection of current technologies. Such rare taxa may make significant contributions to process rates (Shade and Gilbert 2015; Dawson et al. 2017), but their scarcity complicates their identification and analysis. Finally, the vast amounts of information generated through holistic analyses of soil communities represent an intense computational burden (Scholz, Lo, and Chain 2012; Prosser 2015) that precludes assessment of the complete functional and taxonomic diversity contained in this ecosystem.

Naylor, Dan T.↗

DOE OSTI2025

Unraveling the ecological success of Iodidimonas in a bioreactor treating oil and gas produced water

Iodidimonas sp., a bacterium found in bioreactors treating oil and gas produced water as well as iodide-rich brines, has garnered attention for its unique ability to oxidize iodine. However, little is known about the metabolic capabilities that enable Iodidimonas sp. to thrive in certain unique ecological niches. In this study, we isolated, characterized, and sequenced three strains belonging to the Iodidimonas genus from the sludge of a membrane bioreactor used for produced water treatment. We investigated the genomic features of these isolates and compared them with the four publicly available isolate genomes from this genus, as well as a metagenome-assembled genome from the source bioreactor. Our Iodidimonas isolates had several genes associated with mitigating salinity, heavy metal, and organic compound stress, which likely help these bacteria to survive in produced water. Phenotyping tests revealed that while the isolates could utilize a wide variety of simple carbon substrates, they failed to degrade aliphatic or aromatic hydrocarbons, consistent with the lack of genes associated with common hydrocarbon degradation pathways in their genomes. We hypothesize that these microbes may lead a scavenging lifestyle in the bioreactor and similar iodide-rich brines. IMPORTANCE: Occupying a niche habitat and having few representative isolates, the genus Iodidimonas is a relatively understudied alphaproteobacterial group. Its ability to corrode pipes in iodine production facilities has economic implications, and its ability to generate potentially carcinogenic iodinated organic compounds during treatment of oil and gas produced water may cause environmental and health concerns with the recycling of treated water. Therefore, detailed characterization of the metabolic potential of the Iodidimonas isolates in this study both sheds light on their adaptation to the environmental conditions they inhabit and has environmental and economic significance.

Acharya, Shwetha M↗

DOE OSTI2022

TCF High Efficiency Anaerobic Electroporation

09 BIOMASS FUELS↗

DOE OSTI2022

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA). Final report

The goal of the Stahl lab is to use a combination of isotopic, genomic, and activity-based analyses in the field, of selected field isolates, and defined synthetic communities to identify sources and sinks of different nitrogen species in the field, focusing on the FRC at the ORNL. The most general research objective is to characterize variants in the pathway for denitrification among field isolates and synthetic microbial assemblies as a foundation for predicting the biotic and abiotic controls of nitrogen and carbon transformations in the field. Specifically, we have focused on characterizing environmental controls of nitrous oxide emissions, an important greenhouse gas and ozone depleting molecule. Studies have mapped the flux of nitrous oxide and controlling genetic elements within the FRC subsurface, indicating the importance of different enzyme variants in nitrous oxide production and consumption in controlling surface emissions. We have developed methods to quantify and catalog the isotopic signatures imparted on nitrous oxide by different nitrous oxide reductase variants in isolated organisms and model synthetic communities. We have developed methods to quantify and catalog the nitrous oxide affinity of field relevant isolates and their biomass yield when respiring nitrous oxide on different carbon substrates. We continue to expand the collection of field-relevant microbial isolates within ENIGMA by focused enrichment and isolation from field material. These objectives have been facilitated by the development of new technologies, including: 1) the development of a multiplexed automated optical density measurement system for quantifying growth kinetics of microorganisms dependent on gaseous substrates in monoculture or gas exchange in synthetic communities and 2) the development of a microcalorimetric analysis format to quantify the impact of environmental stress on microbial maintenance energy. Since field relevant processes are mediated by assemblies of organisms interacting with each other and their local environment, we have also collaborated with other ENIGMA investigators on the assembly and characterization of synthetic communities. These studies have evaluated the role of organisms lacking a complete pathway for denitrification in the control of field processes, measuring process rates of assemblies of organisms that individually lack the full denitrification pathway but mediate the complete denitrification when growing together. These efforts have so far resulted in the publication of 18 peer reviewed papers ranging from ecological and physiological drivers of pathway optimization to field-scale process characterization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

TCF High Efficiency Anaerobic Electroporation (CRADA Final Report)

The Joint BioEnergy Institute (JBEI) researchers were co-inventors of the technology that will be used on this project and have developed a more current version of the chip and controller. JBEI will also assist with the design of the pathways and implementation of pathways on the chip. LanzaTech has developed novel gas fermentation technology that captures and utilizes greenhouse gases for production of fuels and chemicals. In contrast to traditional fermentation that uses sugars as substrate (and releases CO2 as a byproduct), gas fermentation utilizes C1 substrates carbon monoxide (CO) or CO2. This enables a diverse range of feedstock options including waste gases from industrial sources (e.g., steel mills and processing plants) or syngas generated from any biomass resource (e.g., agricultural waste, municipal solid waste, or organic industrial waste). Biomass is then gasified, allowing for maximum yields and complete carbon utilization including the recalcitrant lignocellulosic fraction that cannot be utilized in traditional sugar fermentation. To maximize the value that can be added to the array of gas resources that the LanzaTech process can use as an input, LanzaTech has pioneered genetic modification of acetogens and developed a comprehensive set of genetic tools to perform routine strain modification, including genome editing tools as CRISPR/Cas9 and libraries of validated genetic parts as promoters and terminators. Using this platform, production of over 50 new molecules have been demonstrated directly from gas. For a few selected molecules production rates and yields have been optimized and surpass production of native producers and engineered E. coli or yeast strains, but a higher throughput approach for combinatorial optimization of pathways is required to further advance synthesis of additional products in parallel.

09 BIOMASS FUELS↗

NASA NTRS1967

An improved standard specimen for alignment of electron microscopes.

Vacuum evaporated tin microscopic particles on carbon substrate used as standard for electron microscope alignment

Carson, K. R.↗

NASA NTRS1974

Further development of chemical vapor deposition process for production of large diameter carbon-base monofilaments

The development of large diameter carbon-base monofilament in the 50 micron to 250 micron diameter range using the chemical vapor deposition process is described. The object of this program was to determine the critical process variables which control monofilament strength, monofilament modulus, and monofilament diameter. It was confirmed that wide scatter in the carbon substrate strength is primarily responsible for the scatter in the monofilament strength. It was also shown through etching experiments that defective substrate surface conditions which can induce low strength modular growth in the monofilament layers are best controlled by processing improvements during the synthesis of the substrate. Modulus was found to be linearily proportional to monofilament boron content. Filament modulus was increased to above 27.8MN/sq cm but only by a considerable increase in monofilament boron content to 60 wt. % or more. Monofilament diameter depended upon dwell time in the synthesis apparatus. A monofilament was prepared using these findings which had the combined properties of a mean U.T.S. of 398,000 N/sq cm, a modulus of 18.9 MN/sq cm (24,000,000 psi), and a diameter of 145 microns. Highest measured strength for this fiber was 451,000 N/sq cm (645,000 psi).

Hough, R. L.↗

NASA NTRS1975

Stopping cross sections for 0.25-3.0-MeV He-4 ions in cadmium sulfide

Stopping cross sections of He-4 ions with energies between 0.25 and 3.0 MeV have been measured for cadmium sulfide with a probable error of plus or minus 7% to 8%. The experimental method utilized the Rutherford backscattering technique and measured the energy loss of elastically scattered He-4 ions from films of cadmium sulfide sputtered on carbon substrates. The experimental data are compared with recent experimental and theoretical results.

Miller, W. E.↗

NASA NTRS1978

Assessment of free-living nitrogen fixing microorganisms for commercial nitrogen fixation

Ammonia production by Klebsiella pneumoniae is not economical with present strains and improving nitrogen fixation to its theoretical limits in this organism is not sufficient to achieve economic viability. Because the value of both the hydrogen produced by this organism and the methane value of the carbon source required greatly exceed the value of the ammonia formed, ammonia (fixed nitrogen) should be considered the by-product. The production of hydrogen by KLEBSIELLA or other anaerobic nitrogen fixers should receive additional study, because the activity of nitrogenase offers a significant improvement in hydrogen production. The production of fixed nitrogen in the form of cell mass by Azotobacter is also uneconomical and the methane value of the carbon substrate exceeds the value of the nitrogen fixed. Parametric studies indicate that as efficiencies approach the theoretical limits the economics may become competitive. The use of nif-derepressed microorganisms, particularly blue-green algae, may have significant potential for in situ fertilization in the environment.

Stokes, B. O.↗

NASA NTRS1979

Hydrogen atom initiated chemistry

H Atoms have been created by the photolysis of H2S. These then initiated reactions in mixtures involving acetylene-ammonia-water and ethylene-ammonia-water. In the case of the acetylene system, the products consisted of two amino acids, ethylene and a group of primarily cyclic thio-compounds, but no free sulfur. In the case of the ethylene systems, seven amino acids, including an aromatic one, ethane, free sulfur, and a group of solely linear thio-compounds were produced. Total quantum yields for the production of amino acids were about 3 x 10 to the -5th and about 2 x 10 to the -4th with ethylene and acetylene respectively as carbon substrates. Consideration is given of the mechanism for the formation of some of the products and implications regarding planetary atmosphere chemistry, particularly that of Jupiter, are explored.

Hong, J. H.↗

NASA NTRS1979

Completion of the Viking Labeled Release experiment on Mars

The final Labeled Release (LR) cycle on each Viking lander tested a surface sample that had been stored for several months at approximately 10 C prior to the onset of the active sequence. At each lander site, activity was strongly diminished. This thermal sensitivity of the active agent on the surface of Mars is consistent with a biological explanation of the LR experiment. At the end of one of these cycles, the incubation mixture was heated to 50 C to release any radioactive gas trapped in the sample matrix. The results suggest that more than one carbon substrate is involved in the LR reaction on Mars. The thermal data from the stored samples, coupled with data from previous cycles, have formed the basis for evaluation of the thermal decomposition of the Mars active agent. The slope of the resulting Arrhenius plot has been used to test the fit of other flight data and to calculate the activation energy for thermal decomposition of the Mars agent. The results and their interpretation still leave unresolved the question of whether the Mars LR data were generated by biological or chemical activity.

Levin, G. V.↗

NASA NTRS1996

Redox Disproportionation of Glucose as a Major Biosynthetic Energy Source

Previous studies have concluded that very little if any energy is required for the microbial biosynthesis of amino acids and lipids from glucose -- processes that yield almost as much ATP (adenosine triphosphate) as they consume. However, these studies did not establish the strength nor the nature of the energy source driving these biological transformations. To identify and estimate the strength of the energy source behind these processes, we calculated the free energy change due to the redox disproportionation of substrate carbon of (a) 26 redox-balanced fermentation reactions, and (b) the biosynthesis of amino acids, lipids, and nucleotides of E. coli from glucose. A plot of the negative free energy of these reactions per mmole of carbon as a function of the number of disproportionative electron transfers per mmol of carbon showed that the energy yields of these fermentations and biosyntheses were directly proportional to the degree of redox disproportionation of carbon. Since this linear relationship showed that redox disproportionation was the dominant energy source of these reactions, we were able to establish that amino acid and lipid biosynthesis obtained most of their energy from redox disproportionation (greater than 94%). In contrast nucleotide biosynthesis was not driven by redox disproportionation of carbon, and consequently depended completely on ATP for energy. This crucial and previously unrecognized role of sugars as an energy source of biosynthesis suggests that sugars were involved at the earliest stage in the origin of anabolic metabolism.

Weber, Arthur L.↗

NASA NTRS1994

Amorphous to Amorphous Form Transitions of Water Ice and Astrophysical Implications

We have combined Selected Area Electron Diffraction (SAED) and cryogenic techniques in an instrumental configuration that allows observing the structure of vapor deposited ice as it evolves during warmup. The ice is deposited in-situ inside an Hitachi H-500 H transmission electron microscope at a base pressure of 1-5 x 10(exp -7) torr on a thin amorphous carbon substrate at 15K or 86K and warmed up at a rate of 1-2 K/min. We find a progression of amorphous forms and well defined amorphous to amorphous transitions. Apart from the well known low-density form of ice, we confirm the presence of a high-density form and find a third amorphous form that coexists with cubic ice. We will report too on the amorphous to crystalline transition and the implications of these results for radical diffusion and gas retention observed in laboratory analog studies of interstellar and cometary ices.

Jenniskens, Peter↗

NASA NTRS1995

The Metastable Persistence of Vapor-Deposited Amorphous Ice at Anomalously High Temperatures

Studies of the gas release, vaporization behavior and infrared (IR) spectral properties of amorphous and crystalline water ice have direct application to cometary and planetary outgassing phenomena and contribute to an understanding of the physical properties of astrophysical ices. Several investigators report anomalous phenomena related to the warming of vapor-deposited astrophysical ice analogs. However gas release, ice volatilization and IR spectral features are secondary or tertiary manifestations of ice structure or morphology. These observations are useful in mimicking the bulk physical and chemical phenomena taking place in cometary and other extraterrestrial ices but do not directly reveal the structural changes which are their root cause. The phenomenological interpretation of spectral and gas release data is probably the cause of somewhat contradictory explanations invoked to account for differences in water ice behavior in similar temperature regimes. It is the microstructure, micromorphology and microchemical heterogeneity of astrophysical ices which must be characterized if the mechanisms underlying the observed phenomena are to be understood. We have been using a modified Transmission Electron Microscope to characterize the structure of vapor-deposited astrophysical ice analogs as a function of their deposition, temperature history and composition. For the present experiments, pure water vapor is deposited at high vacuum onto a 15 K amorphous carbon film inside an Hitachi H-500H TEM. The resulting ice film (approx. 0.05 micrometers thick) is warmed at the rate of 1 K per minute and diffraction patterns are collected at 1 K intervals. These patterns are converted into radial intensity distributions which are calibrated using patterns of crystalline gold deposited on a small part of the carbon substrate. The small intensity contributed by the amorphous substrate is removed by background subtraction. The proportions of amorphous and crystalline material in each pattern are determined by subtracting a percentage of crystalline component relative to amorphous and pure crystalline endmembers. Vapor-deposited water ice undergoes two amorphous to amorphous structural transformations in the temperature range 15-130 K with important astrophysical implications. The onset of cubic crystallization occurs at 142-160 K (at 1K per minute heating rates) during which the 220 and 311 diffraction maxima appear and 0.1 micrometer crystallites can be seen in bright field images. This transition is time dependent.

Blake, David F.↗

NASA NTRS2005

Effects of artificial defoliation of pines on the structure and physiology of the soil fungal community of a mixed pine-spruce forest

Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P < 0.001); the frequency of members of the ectomycorrhizal fungus genus Cenococcum decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P < 0.001) in the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.

Pinus/growth & development/physiology↗

NASA NTRS2006

Oxidation Microstructure Studies of Reinforced Carbon/Carbon

Laboratory oxidation studies of reinforced carbon/carbon (RCC) are discussed with particular emphasis on the resulting microstructures. This study involves laboratory furnace (500-1500 C deg) and arc-jet exposures (1538 C deg) on various forms of RCC. RCC without oxidation protection oxidized at 800 and 1100 C deg exhibits pointed and reduced diameter fibers, due to preferential attack along the fiber edges. RCC with a SiC conversion coating exhibits limited attack of the carbon substrate at 500, 700 and 1500 C deg. However samples oxidized at 900, 1100, and 1300 C deg show small oxidation cavities at the SiC/carbon interface below through-thickness cracks in the SiC coating. These cavities have rough edges with denuded fibers and can be easily distinguished from cavities created in processing. Arc-jet tests at 1538 C deg show limited oxidation attack when the SiC coating and glass sealants are intact. When the SiC/sealant protection system is damaged, attack is extensive and proceeds through matrix cracks, creating denuded fibers on the edges of the cracks. Even at 1538 C deg, where diffusion control dominates, attack is non-uniform with fiber edges oxidizing in preference to the bulk fiber and matrix.

Jacobson, Nathan S.↗

NASA NTRS2009

Recent Shuttle Post Flight MMOD Inspection Highlights

Post flight inspections on the Space Shuttle Atlantis conducted after the STS-11.5 mission revealed a 0.11 inch (2.8 mm) hole in the outer face sheet of the starboard payload bay door radiator panel #4. The payload bay door radiators in this region are 0.5 inch (12.7 mm) thick aluminum honeycomb with 0.011 in (0.279 mm) thick aluminum face sheets topped with 0.005 in (0.127 mm) silver-Teflon tape. Inner face sheet damage included a 0.267 in (6.78 mm) long through crack with measureable deformation in the area of 0.2 in (5.1 mm). There was also a 0.031 in (0.787 nun) diameter hole in the rear face sheet. A large approximately l in (25 mm) diameter region of honeycomb was also destroyed. Since the radiators are located on the inside of the shuttle payload bay doors which are closed during ascent and reentry, the damage could only have occurred during the on-orbit portion of the mission. During the August 2007 STS-118 mission to the International Space Station, a micro-meteoroid or orbital debris (MMOD) particle impacted and completely penetrated one of shuttle Endeavour's radiator panels and the underlying thermal control system (TCS) blanket, leaving deposits on (but no damage to) the payload bay door. While it is not unusual for shuttle orbiters to be impacted by small MMOD particles, the damage from this impact is larger than any previously seen on the shuttle radiator panels. One of the largest impacts ever observed on a crew module window occurred during the November 2008 STS-126 mission to the International Space Station. Damage to the window was documented by the crew on orbit. Post flight inspection revealed a 0.4 in (10.8 mm) crater in the window pane, with a depth of 0.03 in (0.76 mm). The window pane was replaced due to the damage caused by this impact. Analysis performed on residue contained in dental mold impressions taken of the site indicated that a meteoroid particle produced this large damage site. The post flight inspection after the subsequent mission, STS-119 in March of 2009, produced a large MMOD impact feature in a wing leading edge reinforced carbon-carbon panel. The crater measured 0.18 in (4.5 nun) in diameter and was nearly 0.037 in (0.93 nun) deep. The thickness of the silicon carbide coating that protects the carbon substrate is nominally 0.02 in (0.5 nun) to 0.04 in (1 mm), making this a significant impact into the RCC. The damage occurred on the upper surface of the panel, which experiences lower heat loads on re-entry. This poster will document the data collected from the impact sites and will include results of the Scanning Electron Microscope/Energy Dispersive X-ray (SEM/EDX) analysis. Evidence will be presented that suggests a source of the impacts.

Hyed, James L.↗

NASA NTRSDate not supplied

Bioreactor Development for CO2-Based In Situ Resource Utilization Manufacturing

Sustainable long-duration manned missions on both the Moon and Mars will require in situ resource utilization (ISRU). Carbon dioxide (CO2) has great potential as a harvestable resource, making up 95% of the atmosphere on Mars and being produced as respiratory waste in spacecraft and future planetary habitats. Through ISRU, biomanufacturing has the capability to produce a near limitless array of products from local space resources, which include pharmaceuticals, bioplastics, chemical feedstocks, and industrial enzymes. Here, a CO2-based ISRU recombinant protein bioreactor and associated biomanufacturing organisms were designed to produce a highly stable carbonic anhydrase (CA). Initial work characterized candidate organisms for growth on acetate and formic acid, carbon substrates that can be synthesized via electrochemical conversion of CO2. To improve growth on the CO2 producing substrate formic acid and for direct integration of ISRU CO2, a synthetic Calvin-Benson-Bassam cycle was designed for use in Cyberlindnera jadinii and Escherichia coli. Genetic modifications in E. coli will be facilitated by a tailored CRISPR/Cas9 and λ red recombineering two-vector system. For expression of CA, a blue light regulated T7 promoter was employed for dynamic and small molecule free induction. Efficient bioproduction through a fed-batch exponential feeding strategy was determined via mass balance calculations from ISRU substrates to biomass and CA yield. Flux balance analysis was used to model ISRU substrate metabolism and metabolic pathway engineering in candidate organisms under cultivation strategy conditions for both metabolism reconstruction and pathway design optimization. Finally, a small-scale, disposable bag bioreactor concept for use in the NASA Bioculture System infrastructure was designed to enable CO2-based CA production in reduced-gravity environments.

Biomanufacturing, Pathway Engineering, Flux Balanc↗