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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of ~89 years for 1 km depth and 27 C and 1 2 years for 3 km depth and 54 C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.

Onstott, T. C.↗
NASA NTRS2013

Does Aspartic Acid Racemization Constrain the Depth Limit of the Subsurface Biosphere?

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of approximately 89 years for 1 km depth and 27 C and 1-2 years for 3 km depth and 54 C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.

cellular↗
DOE OSTI2016

Physical and hydraulic properties of modern sinter deposits: El Tatio, Atacama

We report sinters are siliceous, sedimentary deposits that form in geothermal areas. Formation occurs in two steps. Hot water circulates in the subsurface and dissolves silica from the host rock, usually rhyolites. Silica then precipitates after hot water is discharged and cools. Extensive sinter formations are linked to up-flow areas of fluids originating from high temperature (> 175 °C) deep reservoirs. Fluid geochemistry, microbial communities, and environmental conditions of deposition determine the texture of sinter and pore framework. Porosity strongly influences physical and hydraulic properties of rocks. To better understand the properties controlling the transport of fluids, and interpret geophysical observations in geothermal systems, here we studied 17 samples of modern geyserite sinter deposits (< 10 ka) from the active El Tatio geothermal field in northern Chile. We measured the physical properties (hydraulic, seismic, and electrical), and internal microstructure (using μX-Ray computed tomography). We find that the pore structure, and thus hydraulic and physical properties, is controlled by the distribution of microbial matter. Based on velocity-porosity relationships, permeability-porosity scaling, and image analysis of the 3D pore structure; we find that the physical and hydraulic properties of sinter more closely resemble those of vesicular volcanic rocks and other material formed by precipitation in geothermal settings (i.e., travertine) than clastic sedimentary rocks.

15 GEOTHERMAL ENERGY↗
DOE OSTI2016

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock

A significant fraction (~ 20%) of microbial life is found in the terrestrial deep subsurface, yet the metabolic processes extant in those environments are poorly understood. Here we show that H 2 , injected into the Opalinus Clay formation in a borehole located 300 meters below the surface, fuels a community of microorganisms with interconnected metabolisms. Metagenomic binning and metaproteomic analysis reveal a complete carbon cycle, driven by autotrophic hydrogen oxidizers. Dead biomass from these organisms is a substrate for a fermenting bacterium that produces acetate as a product. In turn, complete oxidizer heterotrophic sulfate- reducing bacteria utilize acetate and oxidize it to CO 2 , closing the cycle. This metabolic reconstruction sheds light onto a hydrogen-driven carbon cycle, and a sunlight-independent ecosystem in the deep subsurface.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Intrabasin Comparison of the Microbiology and Geochemistry of Produced Fluid From Hydraulically Fractured Wells in the Permian Region

The Permian Basin is the highest producing oil reservoir in the United States. Hydrocarbon extraction methods in this region are often associated with frac hits, or interwell communication events where an established well is affected by the pumping of fracture fluid into a new well. Our previous work revealed a geochemical signal indicating the presence of frac hits in the Permian Basin. We returned to this area with the goal of expanding our understanding of subsurface interactions common in this region. To do so, we collected produced water from 25 unique sites across the Permian Basin, 10 of which had previously been characterized during an active frac hit. For each sample, we measured the pH, alkalinity, geochemistry, microbial load, and microbial community composition. Permian Basin produced water is characterized by higher sulfate and lower total dissolved solids (TDS) concentrations compared to other regions. Interestingly, wells impacted by frac hits have a geochemical profile that resembles that of fracture fluid, with both lowered sulfate and lowered TDS concentrations compared to unaffected wells. Due to the year-long recovery window between sample collection periods, we anticipate that all our data will be characterized by the typical high sulfate, low TDS concentrations.

geochemistry↗
DOE OSTI2015

SFA 2.0- Metabolic Potential

Berkeley Lab Earth Scientists Jill Banfield and Harry Beller explain the Sustainable Systems SFA 2.0 project's research on metabolic potential—or how metabolic lifestyles of microbial communities modulate in response to as well as influence environmental change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Accessing the Subsurface Biosphere Within Rocks Undergoing Active Low-Temperature Serpentinization in the Samail Ophiolite (Oman Drilling Project)

The Oman Drilling Project established an “Active Alteration” multi-borehole observatory in peridotites undergoing low-temperature serpentinization in the Samail Ophiolite. The highly serpentinized rocks are in contact with strongly reducing fluids. Distinct hydrological regimes, governed by differences in rock porosity and fracture density, give rise to steep redox (Eh +200 to –750 mV) and pH (pH range 8.5–11.2) gradients within the 300–400 m deep boreholes. The serpentinites and fluids host an active subsurface ecosystem. Microbial cell abundances in serpentinite vary at least six orders of magnitude, from ≤3.5 × 10 1 to 2.9 × 10 7 cells/g. Low levels of biological sulfate reduction (2–1,000 fmol/cm 3 /day) can be detected in rock cores, particularly in rocks in contact with reduced groundwaters with pH < 10.5. Thermodesulfovibrio is the predominant sulfate reducer identified via metagenomic sequencing of adjacent groundwater communities. Here, we infer that transport and reaction of microbially generated sulfide with the serpentine and brucite assemblages gives rise to optical darkening and sulfide overprinting, including the formation of tochilinite-vallerite group minerals, potentially serving as an indicator that this system is inhabited by microbial life. Olivine mesh-cores replaced with ferroan brucite and minor awaruite, abundant veins containing hydroandradite garnet and polyhedral serpentine, and late-stage carbonate veins are suggested as targets for future spatially resolved life-detection investigations. The high-quality whole-round core samples that have been preserved can be further probed to define how life distributes itself and functions within a system where chemical disequilibria are sustained by low-temperature water/rock interaction, and how biosignatures of in situ microbial activity are generated.

58 GEOSCIENCES↗
DOE OSTI2016

Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments

Riverbed microbial communities play an oversized role in many watershed ecosystem functions, including the processing of organic carbon, cycling of nitrogen, and alterations to metal mobility. The structure and activity of microbial assemblages depend in part on geochemical conditions set by river-groundwater exchange or hyporheic exchange. In order to assess how seasonal changes in river-groundwater mixing affect these populations in a snowmelt-dominated fluvial system, vertical sediment and pore water profiles were sampled at three time points at one location in the hyporheic zone of the Colorado River and analyzed by using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling. Oxic river water penetrated deepest into the subsurface during peak river discharge, while under base flow conditions, anoxic groundwater dominated shallower depths. Over a 70 cm thick interval, riverbed sediments were therefore exposed to seasonally fluctuating redox conditions and hosted microbial populations statistically different from those at both shallower and deeper locations. Additionally, microbial populations within this zone were shown to be the most dynamic across sampling time points, underlining the critical role that hyporheic mixing plays in constraining microbial abundances. Given such mixing effects, we anticipate that future changes in river discharge in mountainous, semiarid western U.S. watersheds may affect microbial community structure and function in riverbed environments, with potential implications for biogeochemical processes in riparian regions.

16S rRNA↗
DOE OSTI2013

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

Increasing evidence emerged for non-random spatial distributions for microbes, but the underlying processes resulting in microbial assemblage variation among and within Earth’s ecosystems is still lacking. For instance, some studies showed that the deterministic processes by habitat specialization are important, while other studies hold that bacterial communities are assembled by neutral forces. Here we examine the relative importance of deterministic and stochastic processes for bacterial communities from subsurface environments, as well as stream biofilm, lake water, lake sediment and soil using pyrosequencing of 16S rRNA gene. We show that there is a general pattern in phylogenetic signal in species niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups, and for three sample groups, that spatial distance reflects unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.

Bacteria↗
NASA NTRS1993

Microscale characterization of dissolved organic matter production and uptake in marine microbial mat communities

Intertidal marine microbial mats exhibited biologically mediated uptake of low molecular weight dissolved organic matter (DOM), including D-glucose, acetate, and an L-amino acid mixture at trace concentrations. Uptake of all compounds occurred in darkness, but was frequently enhanced under natural illumination. The photosystem 2 inhibitor, 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU) generally failed to inhibit light-stimulated DOM uptake. Occasionally, light plus DCMU-amended treatments led to uptake rates higher than light-incubated samples, possibly due to phototrophic bacteria present in subsurface anoxic layers. Uptake was similar with either 3H- or 14C-labeled substrates, indicating that recycling of labeled CO2 via photosynthetic fixation was not interfering with measurements of light-stimulated DOM uptake. Microautoradiographs showed a variety of pigmented and nonpigmented bacteria and, to a lesser extent, cyanobacteria and eucaryotic microalgae involved in light-mediated DOM uptake. Light-stimulated DOM uptake was often observed in bacteria associated with sheaths and mucilage surrounding filamentous cyanobacteria, revealing a close association of organisms taking up DOM with photoautotrophic members of the mat community. The capacity for dark- and light-mediated heterotrophy, coupled to efficient retention of fixed carbon in the mat community, may help optimize net production and accretion of mats, even in oligotrophic waters.

NASA Discipline Exobiology↗
DOE OSTI2025

Identifying Potential Geochemical and Microbial Impacts of Hydrogen Storage in a Deep Saline Aquifer

Hydrogen is valuable commodity and a promising energy carrier for variable energy production. Storage of hydrogen may occur through injection of hydrogen or a hydrogen/methane gas blend in subsurface reservoirs. However, the geochemical and biological reactions that may impact the stored hydrogen are not yet understood. Therefore, we collected samples from a deep storage aquifer located in the St. Peter Formation in southern Illinois. The reservoir material was primarily quartz with sulphur and iron deposits, while the major constituents of the fluid were chloride and sulphate. 16S rRNA gene amplicon sequencing revealed a low biomass microbial community that contained no obvious hydrogen-consuming bacteria. Next, we enriched a field sample to increase the biomass and completed a metagenomic analysis, finding a low number of genes present that are associated with hydrogen consumption. Then, we completed a series of reactor experiments under reservoir conditions with 15% H2/85% CH4 gas simulating a short-term hydrogen storage, high withdrawal scenario. We found minimal changes in the geochemistry or microbiology for the reactor experiments. This work suggests that short-term storage may be highly successful, although significant additional work needs to be completed in order to accurately evaluate the risks associated with long-term hydrogen storage scenarios. It is essential we continue to expand our understanding of the dynamics present in saline aquifers and provide new insights into how hydrogen storage may impact underground geological storage environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology: Metagenomic investigation of the Hellenic Volcanic Arc

Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO 2 -saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Functional metagenomic selection of ribulose 1, 5-bisphosphate carboxylase/oxygenase from uncultivated bacteria

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a critical yet severely inefficient enzyme that catalyses the fixation of virtually all of the carbon found on Earth. Here, we report a functional metagenomic selection that recovers physiologically active RubisCO molecules directly from uncultivated and largely unknown members of natural microbial communities. Selection is based on CO 2 -dependent growth in a host strain capable of expressing environmental deoxyribonucleic acid (DNA), precluding the need for pure cultures or screening of recombinant clones for enzymatic activity. Seventeen functional RubisCO-encoded sequences were selected using DNA extracted from soil and river autotrophic enrichments, a photosynthetic biofilm and a subsurface groundwater aquifer. Notably, three related form II RubisCOs were recovered which share high sequence similarity with metagenomic scaffolds from uncultivated members of the Gallionellaceae family. One of the Gallionellaceae Rubis COs was purified and shown to possess CO 2 /O 2 specificity typical of form II enzymes. X-ray crystallography determined that this enzyme is a hexamer, only the second form II multimer ever solved and the first RubisCO structure obtained from an uncultivated bacterium. Functional metagenomic selection leverages natural biological diversity and billions of years of evolution inherent in environmental communities, providing a new window into the discovery of CO 2 -fixing enzymes not previously characterized.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Coupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species

Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2 - water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Bicarbonate impact on U(VI) bioreduction in a shallow alluvial aquifer

Field-scale biostimulation and desorption tracer experiments conducted in a uranium (U) contaminated, shallow alluvial aquifer have provided insight into the coupling of microbiology, biogeochemistry, and hydrogeology that control U mobility in the subsurface. Initial experiments successfully tested the concept that Fe-reducing bacteria such as Geobacter sp. could enzymatically reduce soluble U(VI) to insoluble U(IV) during in situ electron donor amendment (Anderson et al., 2003; Williams et al., 2011). In parallel, in situ desorption tracer tests using bicarbonate amendment demonstrated rate-limited U(VI) desorption (Fox et al., 2012). These results and prior laboratory studies underscored the importance of enzymatic U(VI)-reduction and suggested the ability to combine desorption and bioreduction of U(VI). Here in this paper we report the results of a new field experiment in which bicarbonate-promoted uranium desorption and acetate amendment were combined and compared to an acetate amendment-only experiment in the same experimental plot. Results confirm that bicarbonate amendment to alluvial aquifer sediments desorbs U(VI) and increases the abundance of Ca-uranyl-carbonato complexes. At the same time, the rate of acetate-promoted enzymatic U(VI) reduction was greater in the presence of added bicarbonate in spite of the increased dominance of Ca-uranyl-carbonato aqueous complexes. A model-simulated peak rate of U(VI) reduction was ~3.8 times higher during acetate-bicarbonate treatment than under acetate-only conditions. Lack of consistent differences in microbial community structure between acetate-bicarbonate and acetate-only treatments suggest that a significantly higher rate of U(VI) reduction in the bicarbonate-impacted sediment may be due to a higher intrinsic rate of microbial reduction induced by elevated concentrations of the bicarbonate oxyanion. The findings indicate that bicarbonate amendment may be useful in improving the engineered bioremediation of uranium in aquifers.

58 GEOSCIENCES↗
DOE OSTI2020

Geochemistry, RNA radiocarbon signature, and metatranscriptome data from Rifle, Colorado groundwater well

Understanding the different sources of carbon subsurface microbes use is highly informative yet remains challenging. The goal of this work was to develop and test a cultivation-independent method that analyzes both the radiocarbon and ribosomal RNA (rRNA) signature of unamplified RNA from the same environmental sample, and that collectively characterizes community carbon utilization under in situ conditions. The method was applied to a filtered groundwater sample from a geochemically reduced zone of a shallow alluvial aquifer near Rife, Colorado (CO), where multiple potential carbon sources co-occur. The radiocarbon and RNA-Seq results, while addressing diverse sample properties, indicated a strikingly similar conclusion about the quantitative role of autotrophy in the subsurface microbial community.This data package provides (1) ribosomal RNA (rRNA) sequences for groundwater microbial populations, (2) the taxonomic identity and relative abundance of groundwater microbial populations based on these rRNA sequences, (3) radiocarbon signatures of the rRNA indicating the source of carbon used by the groundwater microbial populations (provided in both Word docx file and pdf file), (4) geochemical measurements for the monitoring well corresponding to these measurements.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Development of a Knowledgebase to Integrate, Analyze, Distribute, and Visualize Microbial Community Systems Biology Data

We have developed a flexible knowledgebase system, ggKbase, (http://gg.berkeley.edu), to enable effective data analysis and knowledge generation from samples from which metagenomic and other ‘omics’ data are obtained. Within ggKbase, data can be interpreted, integrated and linked to other databases and services. Sequence information from complex metagenomic samples can be quickly and effectively resolved into genomes and biologically meaningful investigations of an organism’s metabolic potential can then be conducted. Critical features make analyses efficient, allowing analysis of hundreds of genomes at a time. The system is being used to support research in multiple DOE-relevant systems, including the LBNL SFA subsurface science biogeochemical cycling research at Rifle, Colorado. ggKbase is supporting the research of a rapidly growing group of users. It has enabled studies of carbon cycling in acid mine drainage ecosystems, biologically-mediated transformations in deep subsurface biomes sampled from mines and the north slope of Alaska, to study the human microbiome and for laboratory bioreactor-based remediation investigations.

59 BASIC BIOLOGICAL SCIENCES↗