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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Extracellular electron transfer mechanisms between microorganisms and minerals

Electrons can be transferred from microorganisms to multivalent metal ions that are associated with minerals and vice versa. As the microbial cell envelope is neither physically permeable to minerals nor electrically conductive, microorganisms have evolved strategies to exchange electrons with extracellular minerals. In this Review, we discuss the molecular mechanisms that underlie the ability of microorganisms to exchange electrons, such as c-type cytochromes and microbial nanowires, with extracellular minerals and with microorganisms of the same or different species. Microorganisms that have extracellular electron transfer capability can be used for biotechnological applications, including bioremediation, biomining and the production of biofuels and nanomaterials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by microorganisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi and Rokubacteria are understudied. Here, we have resolved 60 metagenomic and 20 proteomic data sets from a Mediterranean grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one-third of all microorganisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. In contrast, most microorganisms encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain the high prevalence of C 1 metabolism and acetate utilization in genomes. Microorganism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall, indicating that long-term climate alteration can affect both carbon and nitrogen cycling. As a whole, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link microorganisms lacking prior genomic characterization to specific roles in complex carbon, C 1 , nitrate and ammonia transformations, and constrain factors that impact their distributions in soil.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Engineered Ureolytic Microorganisms Can Tailor the Morphology and Nanomechanical Properties of Microbial-Precipitated Calcium Carbonate

We demonstrate for the first time that the morphology and nanomechanical properties of calcium carbonate (CaCO 3 ) can be tailored by modulating the precipitation kinetics of ureolytic microorganisms through genetic engineering. Many engineering applications employ microorganisms to produce CaCO 3 . However, control over bacterial calcite morphology and material properties has not been demonstrated. We hypothesized that microorganisms genetically engineered for low urease activity would achieve larger calcite crystals with higher moduli. We compared precipitation kinetics, morphology, and nanomechanical properties for biogenic CaCO 3 produced by two Escherichia coli ( E. coli ) strains that were engineered to display either high or low urease activity and the native producer Sporosarcina pasteurii . While all three microorganisms produced calcite, lower urease activity was associated with both slower initial calcium depletion rate and increased average calcite crystal size. Both calcite crystal size and nanoindentation moduli were also significantly higher for the low-urease activity E. coli compared with the high-urease activity E. coli . The relative resistance to inelastic deformation, measured via the ratio of nanoindentation hardness to modulus, was similar across microorganisms. These findings may enable design of novel advanced engineering materials where modulus is tailored to the application while resistance to irreversible deformation is not compromised.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Documenting the function of non-cultivated microorganisms in terrestrial ecosystems

The terrestrial biosphere contains a large fraction of global carbon and nearly 70% of the organic carbon in these systems is found in soils. Global changes in atmospheric CO 2 , temperature, precipitation, and ecosystem N inputs, are expected to impact primary production and carbon inputs to soils, but it remains difficult to predict the response of soil processes to anthropogenic change. Models that predict soil C-cycling as a function of ecosystem properties do not explain well variation in soil processes. Our difficulty in predicting the response of soil processes to environmental change suggests a need for a greater understanding of the biotic mechanisms that govern the soil C-cycle. Changes in microbial community structure and function have been proposed to impact soil C-cycling. However, our ability to predict the impacts of these changes on terrestrial ecosystems is constrained by our limited understanding of mechanisms that drive microbial processes in soil systems. We have applied a newly developed approach of Microbial Food Web Mapping to chart the carbon assimilation dynamics of microbial taxa in soils. This method made it possible to track different classes of 13C-labeled substrates into the DNA of nearly every member of the soil community simultaneously over time. Microbial Food Web Mapping was used to identify and characterize microbial taxa that fill key roles in the soil carbon cycle. We mapped the assimilation of carbon into thousands of discrete soil microorganisms as a function of soil carbon content and pH. In so doing we characterized assimilatory carbon metabolism, an essential component of soil C-cycling, for a vast array of uncultivated soil microorganisms. Further, we characterized the spatial and temporal dynamics of these microorganisms across a series of sites representing variation in soil characteristics. This project revealed fundamental aspects of soil C-cycling and provided ecological and metabolic insights on diverse uncultivated soil organisms that are widespread and play major roles in the global C-cycle. The genetic capacity of microbial communities can be studied through ‘omic approaches but it remains difficult to make direct links between the genetic capacity of microorganisms and their function in the soil C-cycle. Microbial Food Web Mapping makes it possible to link gene sequences to soil C-cycle processes as they occur in soil. This approach allows us to characterize the activity of non-cultivated microorganisms in a range of terrestrial systems. This data will be used to build a base of information about the role of non-cultivated organisms in critical C-cycle processes in terrestrial ecosystems and will provide insight on the manner in which soil communities metabolize soil organic matter. The results generated by this project will improve our ability to examine the impacts of management decisions, soil history, and environmental change on the behavior of microbial communities in terrestrial ecosystems, revealing the ecological mechanisms by which microbes regulate both C mineralization and carbon retention in soils, and improving our ability to predict changes in terrestrial ecosystem processes in the face of accelerating global change.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2002

Distinguishing Indigenous from Contaminating Microorganisms in Rock Samples from a Deep Au Mine in South Africa

The concentration and distribution of microbial biomass within deep subsurface rock strata is not well known To date, most analyses are from water samples and a few cores. Hand samples, block samples and cores from an actively mined Carbon Leader ore zone at 3.2 kilometers depth were collected for microbial analyses. The Carbon Leader was comprised of quartz, S-bearing aromatic hydrocarbons, Fe(III) oxyhydroxides, sulfides, uraninite, Au and minor amounts of sulfate. The porosity of the ore was 1% and the maximum pore throat diameter was less than 0.1 microns; whereas, the porosity of the adjacent quartzite was .02 to .9% with a maximum pore throat diameter of 0.9 microns. Rhodamine dye, fluorescent microspheres, microbial enrichments, autoradiography, phospholipid fatty acid (PLEA) and 16S rDNA analyses were performed on these rock samples and the mining water. The date indicate that the levels of solute contamination less than 0.01% for pared rock samples. Despite this low level of contamination, PLEA, microbial enrichment, DNA and tracer analyses and calculations indicate that most of the viable microorganisms in the Carbon Leader represent gram negative aerobic heterotrophs and ammonia oxidizers that are phylogenetically identical or closely related to service water microorganisms. These microbial contaminants probably infiltrated the low permeability rock through mining-induced microfractures. Geochemical data also detected drilling water in a fault zone approx. 1 meter behind the rock face encountered during coring. The mining induced macrofractures that are common at these great depths act as pathways for the drilling water borne microorganisms into the lower temperature zone that extends several meters into rock strata from the rock face. Combined PLEA and T- RFLP analyses of the service water and Carbon Leader samples indicate that the concentration of indigenous microorganisms was less than 10(exp 2) cells/gram. Such a low concentrations result from the submicron pore throat diameters. PLFA. SO4-35 autoradiography and tracer analyses indicate that the bounding quartzite contains thermophilic sulfate reducing bacteria at 10(exp 3) cells/gram that are not attributable to drilling water contamination. The microorganisms may be surviving on sulfate generated by oxidation of sulfide by radiolytic reactions resulting from the high U concentration in the ore zone. The presence of up to 8,000 ppm of Fe(III) oxyhydroxides in the host rock will also act to recycle sulfide generated by the sulfate reducing bacteria into sulfate. The activity of these sulfate-reducing bacteria may be enhanced by mining induced fracturing which can propagate up to 40 meters into virgin rock where the temperatures are ca. 50 C, and decrepitate of sulfate rich fluid inclusions. In ultra deep mines, judicious application of tracers and multiple microbial characterization techniques can distinguish microbial contamination caused by the near field fracturing and drilling water migration from the indigenous microbial communities in rock strata. The importance of far field fracturing on indigenous microbial communities, however, remains unknown.

Onstott, T. C.↗
NASA NTRS2003

Identification and Characterization of Extremophile Microorganisms with Significance to Astrobiology

It is now well recognized that microorganisms thrive in extreme ecological conditions such as geothermal vents, polar region, acid and alkaline lakes, and the cold pressurized depth of the ocean floor of this planet. Morphological, physiological, biochemical and genetic adaptations to extreme environments by these extremophile microorganisms have generated immense interest amongst astrobiologists who increasingly believe in the existence of extraterrestrial life. The evidence collected by NASA's space probe Galileo suggested the presence of liquid water and volcanic activity on Mars and Jupiter's satellite Europa. Volcanic activity provides some of the heat necessary to keep the water on Europa from freezing that could provide important dissolved chemicals needed by living organisms. The possibility of the existence of hypersaline alkaline lakes and evaporites confined within closed volcanic basins and impact craters on Mars, and a layer of liquid water under the ice on Europa provide sufficient 'raison d'etre' to study microorganisms in similar extreme environments on Earth, which could provide us with a model that would help establish the existence of extraterrestrial life on other planetary bodies. The objectives of the summer research project were as follows: (1) application of molecular approaches to help establish new species of extremophile microorganisms isolated from a hypersaline alkaline lake; and (2) identification of a major cold-shock gene (cspA) homolog from a psychrotolerant microorganism, PmagG1.

Bej, Asim K.↗
NASA NTRS2002

Comparative Results of Using Different Methods for Discovery of Microorganisms in very Ancient Layers of the Central Antarctic Glacier above the Lake Vostok

The ice sheet of the Central Antarctic is considered by the scientific community worldwide, as a model to elaborate on different methods to search for life outside Earth. This became especially significant in connection with the discovery of the underglacial lake in the vicinity of the Russian Antarctic Station Vostok. Lake Vostok is considered by many scientists as an analog of the ice covered seas of Jupiter's satellite Europa. According to the opinion of many researchers there is the possibility that relict forms of microorganisms, well preserved since the Ice Age, may be present in this lake. Investigations throughout the thickness of the ice sheet above Lake Vostok show the presence of microorganisms belonging to different well-known taxonomic groups, even in the very ancient horizons near close to floor of the glacier. Different methods were used to search for microorganisms that are rarely found in the deep ancient layers of an ice sheet. The method of aseptic sampling from the ice cores and the results of controlled sterile conditions in all stages when conducting these investigations, are described in detail in previous reports. Primary investigations tried the usual methods of sowing samples onto different nutrient media, and the result was that only a few microorganisms grew on the media used. The possibility of isolating the organisms obtained for further investigations, by using modern methods including DNA-analysis, appears to be the preferred method. Further investigations of the very ancient layers of the ice sheet by radioisotopic, luminescence, and scanning electron microscopy methods at different modifications, revealed the quantity and morphological diversity of the cells of microorganisms that were distributed on the different horizons. Investigations over many years have shown that the microflora in the very ancient strata of the Antarctic ice cover, nearest to the bedrock, support the effectiveness of using a combination of different methods to search for signs of life in ancient icy formations, which might play a role in the long-term preservation and transportation of microbial life throughout the Universe.

Abyzov, S. S.↗
NASA NTRS2006

Fossil Microorganisms in Archaean

Ancient Archean and Proterozoic rocks are the model objects for investigation of rocks comprising astromaterials. The first of Archean fossil microorganisms from Baltic shield have been reported at the last SPIE Conference in 2005. Since this confeence biomorphic structures have been revealed in Archean rocks of Karelia. It was determined that there are 3 types of such bion structures: 1. structures found in situ, in other words microorganisms even-aged with rock matrix, that is real Archean fossils biomorphic structures, that is to say forms inhabited early formed rocks, and 3. younger than Archean-Protherozoic minerali microorganisms, that is later contamination. We made attempt to differentiate these 3 types of findings and tried to understand of burial of microorganisms. The structures belongs (from our point of view) to the first type, or real Archean, forms were under examination. Practical investigation of ancient microorganisms from Green-Stone-Belt of Northern Karelia turns to be very perspective. It shows that even in such ancient time as Archean ancient diverse world existed. Moreover probably such relatively highly organized cyanobacteria and perhaps eukaryotic formes existed in Archean world.

Astafleva, Marina↗
DOE OSTI2014

Microorganisms for producing organic acids

Organic acid-producing microorganisms and methods of using same. The organic acid-producing microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid, acrylic acid, propionic acid, lactic acid, and others. Further modifications to the microorganisms increase production of such organic acids as 3-hydroxypropionic acid, lactate, and others. Methods of producing such organic acids as 3-hydroxypropionic acid, lactate, and others with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers are also provided.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Microorganisms for producing organic acids

Organic acid-producing microorganisms and methods of using same. The organic acid-producing microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid, acrylic acid, propionic acid, lactic acid, and others. Further modifications to the microorganisms increase production of such organic acids as 3-hydroxypropionic acid, lactate, and others. Methods of producing such organic acids as 3-hydroxypropionic acid, lactate, and others with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers are also provided.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Microorganisms and methods for producing pyruvate, ethanol, and other compounds

Microorganisms comprising modifications for producing pyruvate, ethanol, and other compounds. The microorganisms comprise modifications that reduce or ablate activity of one or more of pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, phosphate acetyltransferase, acetate kinase, pyruvate oxidase, lactate dehydrogenase, cytochrome terminal oxidase, succinate dehydrogenase, 6-phosphogluconate dehydrogenase, glutamate dehydrogenase, pyruvate formate lyase, pyruvate formate lyase activating enzyme, and isocitrate lyase. The microorganisms optionally comprise modifications that enhance expression or activity of pyruvate decarboxylase and alcohol dehydrogenase. The microorganisms are optionally evolved in defined media to enhance specific production of one or more compounds. Methods of producing compounds with the microorganisms are provided.

09 BIOMASS FUELS↗
DOE OSTI2018

Gene-matched enrichment and polymerase chain reaction for rapid detection of microorganisms

A method for amplifying and detecting microorganisms, such as species of Listeria, is described. The method utilizes gene-matched enrichment media and PCR-based detection. The enrichment media is spent media produced using a modified microorganism containing a plurality of mutations in a selected gene such that the modified microorganism does not contain the PCR signature. Thus, PCR detects only the amplified microorganism of interest, not the modified microorganism. Exemplary methods and kits for amplification and detection of Listeria species are described.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Microorganisms and methods for producing pyruvate, ethanol, and other compounds

Microorganisms comprising modifications for producing pyruvate, ethanol, and other compounds. The microorganisms comprise modifications that reduce or ablate activity of one or more of pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, phosphate acetyltransferase, acetate kinase, pyruvate oxidase, lactate dehydrogenase, cytochrome terminal oxidase, succinate dehydrogenase, 6-phosphogluconate dehydrogenase, glutamate dehydrogenase, pyruvate formate lyase, pyruvate formate lyase activating enzyme, and isocitrate lyase. The microorganisms optionally comprise modifications that enhance expression or activity of pyruvate decarboxylase and alcohol dehydrogenase. The microorganisms are optionally evolved in defined media to enhance specific production of one or more compounds. Methods of producing compounds with the microorganisms are provided.

09 BIOMASS FUELS↗
DOE OSTI2021

Spent enrichment media for growth of gene-matched microorganisms

A method for amplifying and detecting microorganisms, such as species of Listeria, is described. The method utilizes gene-matched enrichment media and PCR-based detection. The enrichment media is spent media produced using a modified microorganism containing a plurality of mutations in a selected gene such that the modified microorganism does not contain the PCR signature. Thus, PCR detects only the amplified microorganism of interest, not the modified microorganism. Exemplary methods and kits for amplification and detection of Listeria species are described.

Ozanich, Richard M.↗
DOE OSTI2021

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Abstract Background Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost. Results Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26–120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost. Conclusions Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2012

Isolation of Phyllosilicate–Iron Redox Cycling Microorganisms from an Illite–Smectite Rich Hydromorphic Soil

The biogeochemistry of phyllosilicate–Fe redox cycling was studied in a Phalaris arundinacea (reed canary grass) dominated redoximorphic soil from Shovelers Sink, a small glacial depression near Madison,WI.The clay size fraction of Shovelers Sink soil accounts for 16% of the dry weight of the soil, yet contributes 74% of total Fe. The dominant mineral in the clay size fraction is mixed layer illite–smectite, and in contrast to many other soils and sediments, Fe(III) oxides are present in low abundance.We examined the Fe biogeochemistry of Shovelers Sink soils, estimated the abundance of Fe redox cycling microorganisms, and isolated in pure culture representative phyllosilicate–Fe oxidizing and reducing organisms. The abundance of phyllosilicate–Fe reducing and oxidizing organisms was low compared to culturable aerobic heterotrophs. Both direct isolation and dilution-to-extinction approaches using structural Fe(II) in Bancroft biotite as a Fe(II) source, and O2 as the electron acceptor, resulted in recovery of common rhizosphere organisms including Bradyrhizobium spp. and strains of Cupriavidus necator and Ralstonia solanacearum. In addition to oxidizing biotite and soluble Fe(II) with O 2 , each of these isolates was able to oxidize Fe(II) in reduced NAu2 smectite with NO$^-_3$ as the electron acceptor. Oxidized NAu-2 smectite or amorphous Fe(III) oxide served as electron acceptors for enrichment and isolation of Fe(III)-reducing microorganisms, resulting in recovery of a strain related to Geobacter toluenoxydans. The ability of the recovered microorganisms to cycle phyllosilicate–Fe was verified in an experiment with native Shovelers Sink clay. This study confirms that Fe in the native Shovelers Sink clay is readily available for microbial redox transformation and can be cycled by the Fe(III)-reducing and Fe(II)-oxidizing microorganisms recovered from the soil.

soil↗
DOE OSTI2020

Recent Advances in Domesticating Non-model Microorganisms

Non-model microorganisms have been increasingly explored as microbial cell factories for production of chemicals, fuels, and materials owing to their unique physiology and metabolic capabilities. Yet, these microorganisms often lack facile genetic tools for strain development, which hinders their adoption as production hosts. In this review, we describe recent advances in domestication of non-model microorganisms, including bacteria, actinobacteria, cyanobacteria, yeast, and fungi, with a focus on the development of genetic tools. Furthermore, we highlight some successful applications of non-model microorganisms as microbial cell factories.

synthetic biology↗
DOE OSTI2010

Role of extracellular polymeric substances in bioflocculation of activated sludge microorganisms under glucose-controlled conditions

Extracellular polymeric substances (EPS) secreted by suspended cultures of microorganisms from an activated sludge plant in the presence of glucose was characterized in detail using colorimetric analysis, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy. EPS produced by the mixed population were similar to literature reports obtained from pure cultures in terms of functionalities with respect to C and O but differed subtly in terms of N and P. Hence, it appears that EPS produced by different microorganisms maybe similar in major chemical constituents but may differ in minor components. The role of specific EPS constituents on microbial aggregation was also determined. The weak tendency of microorganisms to bioflocculate during the exponential growth phase was attributed to electrostatic repulsion when EPS concentration was low and acidic in nature (higher fraction of uronic acids to total EPS). However, during the stationary phase, polymeric interactions overwhelmed electrostatic interactions (lower fraction of uronic acids to total EPS) resulting in greater bioflocculation. More specifically, microorganisms appeared to aggregate in the presence of protein secondary structures including aggregated strands, β-sheets, α- and 3-turn helical structures. Bioflocculation was also favored by increasing O-acetylated carbohydrates and overall C-(O,N) and O=C–OH + O=C–OR functionalities.

59 BASIC BIOLOGICAL SCIENCES↗