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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Novel Geochemistry Determined from High Pressure, High Temperature Simulation Experiments of Hydraulic Fracture Test Site 2

A standard method in unconventional oil and gas production is the process of hydraulic fracturing followed by a shut-in period, during which the fracture fluid remains pressurized in the reservoir for up to three weeks before production begins. Despite this widely used process, very little is known about what occurs in the reservoir during this shut-in process. In order to properly delineate potential reservoir reactions that may occur during shut-in that would lead to corrosion and scaling events, experiments were conducted in high pressure, high temperature reactors to simulate conditions of the Wolfcamp Formation in the Delaware Basin. Experimental design allowed the assessment of the effect of proppant, microbiology, and time on the mineralogy and fluid chemistry in the reservoir. Results suggest the biggest impact on fluid chemistry and shale mineralogy during shut-in is time. Analyses demonstrate dissolution of the shale material, with maximum dissolved ions occurring after 7 days of the shut-in period. After 21 days, results suggest precipitation occurs. The Delaware Basin is demonstrated to be high in sulfate content, which further increases in the fluid due to dissolution reactions during shut-in. The pressure vessel experiments suggest there was no significant contribution to reactions from microbiology during the shut-in period. Furthermore, early production samples demonstrate a significant selection of the microorganism Caminicella, a genus of which has previously been correlated to corrosion and sulfide production. Results suggest shut-in conditions may provide high sulfate concentrations that could later be utilized by a shifted microbial community to drive potential well infrastructure failure. This is the first study to incorporate microbiology, mineralogy, and fluid chemistry to investigate the fundamental geochemical reactions that occur during shut-in and early phase production of the Delaware Downloaded from http://onepetro.org/URTECONF/proceedings-pdf/21URTC/2-21URTC/D021S032R001/2477425/urtec-2021-5219-ms.pdf/1 by Carol Worster on 28 February 2022 Basin. Results from this study can complement observations from the Hydraulic Fracture Test Site 2 observations

58 GEOSCIENCES↗
DOE OSTI2023

Life history strategies among soil bacteria—dichotomy for few, continuum for many

Abstract Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both 18O–H2O and 13C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms’ joint 18O–13C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Plant-specific microbial diversity facilitates functional redundancy at the soil-root interface

Abstract Aims Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (root endosphere, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. The study aimed to examine the impact of the rhizosphere on microbial community composition and diversity in desert agricultural soil, as well as to identify specific functions associated with the rhizosphere. Methods The microbiome community structure, diversity, and microbial functioning were evaluated through the utilization of 16S rRNA gene amplicon and shotgun metagenome sequencing. Results We found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. The annual plants Calendula officinalis and Matricaria chamomilla ( Asteraceae ) were more similar than the perennial Solanum distichum ( Solanaceae ). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in root endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific. Conclusions The study explores the microbiome continuum at the soil-root interface of medicinal plant species, revealing significant bacterial community structure shifts and plant specificity. The study provides insights into the essential microbiome components contributing to rhizosphere functionality.

Wicaksono, Wisnu Adi (ORCID:0000000215561981)↗
DOE OSTI2026

Data for Genetic Variation in Zea mays Influences Microbial Nitrification and DeNitrification in Conventional Agroecosystems

Nitrogenous fertilizers provide a short-lived benefit to crops in agroecosystems, but stimulate nitrification and denitrification, processes that result in nitrate pollution, N2O production, and reduced soil fertility. Recent advances in plant microbiome science suggest that genetic variation in plants can modulate the composition and activity of rhizosphere N-cycling microorganisms. Here we attempted to determine whether genetic variation exists in Zea mays for the ability to influence the rhizosphere nitrifier and denitrifier microbiome under “real-world” conventional agricultural conditions. To capture an extensive amount of genetic diversity within maize we grew and sampled the rhizosphere microbiome of a diversity panel of germplasm that included ex-PVP inbreds ( Z. mays ssp. mays ), ex-PVP hybrids ( Z. mays ssp. may s), and teosinte ( Z. mays ssp. mexicana and Z. mays ssp. parviglumis ). From these samples, we characterized the microbiome, a suite of microbial genes involved in nitrification and denitrification and carried out N-cycling potential assays. Here we are showing that populations/genotypes of a single species can vary in their ecological interaction with denitrifers and nitrifers. Some hybrid and teosinte genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbred genotypes stimulated/did not inhibit these N-cycling activities. These potential differences translated to functional differences in N2O fluxes, with teosinte plots producing less GHG than maize plots. Taken together, these results suggest that Zea genetic variation can lead to changes in N-cycling processes that result in N leaching and N2O production, and thereby are selectable targets for crop improvement. Understanding the underlying genetic variation contributing to belowground microbiome N-cycling into our conventional agricultural system could be useful for sustainability.

Nitrogen↗
DOE OSTI2021

Effect of tectonic processes on biosphere–geosphere feedbacks across a convergent margin

The subsurface is among Earth’s largest biomes, but the extent to which microbial communities vary across tectonic plate boundaries or interact with subduction-scale geological processes remains unknown. Here we compare bacterial community composition with deep-subsurface geochemistry from 21 hot springs across the Costa Rican convergent margin. We find that cation and anion compositions of the springs reflect the dip angle and position of the underlying tectonic structure and also correlate with the bacterial community. Co-occurring microbial cliques related to cultured chemolithoautotrophs that use the reverse tricarboxylic acid cycle (rTCA) as well as abundances of metagenomic rTCA genes correlate with concentrations of slab-volatilized carbon. This, combined with carbon isotope evidence, suggests that fixation of slab-derived CO2 into biomass may support a chemolithoautotrophy-based subsurface ecosystem. We calculate that this forearc subsurface biosphere could sequester 1.4 × 10 9 to 1.4 × 10 10 mol of carbon per year, which would decrease estimates of the total carbon delivered to the mantle by 2 to 22%. Furthermore, based on the observed correlations, we suggest that distribution and composition of the subsurface bacterial community are probably affected by deep tectonic processes across the Costa Rican convergent margin and that, by sequestering carbon volatilized during subduction, these chemolithoautotrophic communities could in turn impact the geosphere.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Role of redox-active biochar with distinctive electrochemical properties to promote methane production in anaerobic digestion of waste activated sludge

Biochar has been reported as an effective additive to improve methane production during anaerobic digestion (AD). However, the mechanism for such a stimulatory impact remains unclear. Here we investigated the capability of three pyrolytic biochars with distinctive electrochemical properties (BC300, BC500, BC700) to promote methanogenic performance of anaerobic digesters treating waste activated sludge (WAS). The cumulative methane production and the maximum methane production rate were increased by 46.9% and 181.6%, respectively, with BC300 amendment. By characterizing the electrochemical properties of biochar, our research team found out that methane production in AD of sludge was positively correlated to biochar’s electron-donating capacity (EDC) rather than its bulk electrical conductivity. These results indicate that the electron transfer mediated by the redox-active functional groups may prevail over the direct electron migration as the predominant mechanism to facilitate interspecies electron transfer in syntrophic communities for enhanced methanogenesis. Microbial community analysis suggests that biochar enriched Methanosarcina and Methanobacterium. Overall, this study shows that functional groups-mediated electron transfer contributes greatly to the improved methane production in WAS digester with biochar amendment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Solutions in microbiome engineering: prioritizing barriers to organism establishment

Abstract Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia

Biofertilizers are critical for sustainable agriculture because they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. However, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. In this study we characterized a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. Here, we profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and we detected significant phylogenetic diversity (e.g. Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated that the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs in which an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in ~10% of SynComs that generally followed the diversity–invasion principle. Additionally, our approach enabled analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work has established a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessment of the persistence of a specific organism of interest and its interaction with native consortia.

biofertilizers↗
DOE OSTI2021

Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in MOPS Medium

This narrative was used for the 4-member community modeling using MOPS medium for the bacteria isolated from Populus deltoides (PD). 10 bacterial strains isolated from PD were co-cultured as a synthetic microbial community in MOPS minimal medium. After 15 passages there were 4 members survived in MOPS medium. The genome of each community member was sequenced and uploaded into KBase for genome annotation and metabolic modeling. To simulate the metabolic interactions among the finally surviving community members, the individual metabolic models of each strain were merged into a compartmentalized community model, and then the community model was gapfilled using MOPS medium. The FBA modeling was performed and the metabolites exchange among community members was proposed. The publication by Jia Wang, Dana L. Carper, Leah H. Burdick, Him Shrestha, Manasa Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz can be found here: https://doi.org/10.​1016/​j.​csbj.​2021.​03.​034

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium

This narrative was used for the 3-member community modeling using R2A medium for the bacteria isolated from Populus deltoides (PD). 10 bacteiral strains isolated from PD were co-cultured as a synthetic microbial community in R2A complex medium. After 15 passages, there were 3 members survived in R2A medium. The genome of each community member was sequenced and uploaded into KBase for genome annotation and metabolic modeling. To simulate the metabolic interactions among the finally surviving community members, the individual metabolic models of each strain were merged into a compartmentalized community model, and then the community model was gapfilled using R2A medium. The FBA modeling was performed and the metabolites exchange among community members was proposed. The publication by Jia Wang, Dana L. Carper, Leah H. Burdick, Him Shrestha, Manasa Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz can be found here: https://doi.org/10.​1016/​j.​csbj.​2021.​03.​034

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

MiNAA: Microbiome Network Alignment Algorithm

A microbial network is a mathematical representation of a microbial community where nodes represent microbes and edges represent interactions. It is well-recognized that microbes are among the main drivers of biological phenotypes in soil, plants, and animals alike, and thus, their study has vast implications for soil, plant and human health. In particular, recognizing the microbial, environmental, and agricultural factors that drive plant and soil phenotypes is crucial to comprehend processes connected to plant and soil health, to identify global practices of sustainable agriculture, as well as to predict plant and soil responses to environmental perturbations such as climate change. The adaptability of microbes to thrive in every environment poses challenges for scientists who try to understand their communities. Indeed, two microbial communities with the exact same players can interact differently depending on the environmental conditions. It is thus desirable to identify commonalities and differences on two microbial networks, hence the need for computational tools that can match (or align) them.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Reduction of microbial diversity in grassland soil is driven by long-term climate warming

Anthropogenic climate change threatens ecosystem functioning. Soil biodiversity is essential for maintaining the health of terrestrial systems, but how climate change affects the richness and abundance of soil microbial communities remains unresolved. Here, we examined the effects of warming, altered precipitation and annual biomass removal on grassland soil bacterial, fungal and protistan communities over 7 years to determine how these representative climate changes impact microbial biodiversity and ecosystem functioning. We show that experimental warming and the concomitant reductions in soil moisture play a predominant role in shaping microbial biodiversity by decreasing the richness of bacteria (9.6%), fungi (14.5%) and protists (7.5%). Our results also show positive associations between microbial biodiversity and ecosystem functional processes, such as gross primary productivity and microbial biomass. We conclude that the detrimental effects of biodiversity loss might be more severe in a warmer world.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Bleach Rescues Nannochloropsis from an Obligate Parasite and Alters Microbial and Metabolite Signatures of Outdoor Cultures

Chemical agents are commonly used to protect algal crops. Yet, few studies have characterized the effects of these agents on associated microbial communities to understand effects on microbial functions relevant to algal crop production and protection. Here, we used shotgun metagenomic sequencing and untargeted exometabolite profiling to link the application of bleach, a -cidal agent used to protect algae from pests, to changes in community composition, metabolic pathways, and exometabolies - at a whole community level. Bleach protected the algal crop from crashing but altered bacterial diversity. Analysis of metagenome-assembled genomes (MAGs) revealed a classic predator-prey cycle between Oligoflexus and our target alga Nannochloropsis. Olifoflexus genomes from our study were notably similar to a previously identified BALO (Bdellovibrio and like organism), FD111, known to kill Nannochloropsis cultures, providing strong evidence that an FD111-like organism was responsible for the crash. Metabolic pathway composition differed between bleached and unbleached ponds, with abundance of twelve pathways related to stress tolerance, including the superpathway of methylglyoxal degradation, lipid IVA biosynthesis, and ectoine biosynthesis, greater in bleached ponds compared to unbleached ponds. Virulence factors related to adherence, biofilm formation, motility, and pathogenicity increased dramatically in bleached ponds with time, although this increase was not coupled with an increase in pathogens - algal or otherwise - or a decline in algal health. Our study highlights the importance of coupling 16S rRNA gene sequencing with whole genome data and other -omics tools to sketch a larger picture of community structure and function in crop systems. Moreover, our results highlight that continued long-term bleaching may lead to negative effects to crop health or downstream adverse health effects to humans or animals, depending on the algal product (i.e. human supplements or animal feedstocks). Future work on alternative treatment methods that would reduce resistance is necessary in the field.

09 BIOMASS FUELS↗
DOE OSTI2022

Watershed-scale liming reveals the short- and long- term effects of pH on the forest soil microbiome and carbon cycling

Soil microbial community composition routinely correlates with pH, reflecting both direct pH effects on microbial physiology and long-term biogeochemical feedbacks. For this work, we used two watershed-scale liming experiments to identify short- (2 years) and long-term (25 years) changes in the structure and function of bacterial and fungal communities in organic horizons (O e and O a ) of acid forest soils. Liming increased soil pH, extractable calcium, and soil carbon stocks, reduced biomass-specific respiration, and caused major changes in the soil microbiome in the short and long term. More taxa responded to liming in the short term (70%) than in the long term (30%), with most showing consistent directional responses at both sites. The ratio of change in relative abundance between limed and reference sites was twofold higher at the long than the short-term site, indicating that the effects of liming grew over time. Liming impacts were most pronounced in fungi, as steep declines of dominant ectomycorrhizal fungi ( Cenococcum and Russula ) occurred at both sites. Liming favoured neutrophilic bacteria over acidophilic populations according to estimated environmental pH optima. Collectively, these results demonstrate that a liming-induced change of one pH unit has an immediate and persistent effect on the structure and function of microbial communities in acid forest soils. The corresponding suppression of respiration indicates that anthropogenic alterations of soil pH, as driven by acid deposition or liming, can affect forest floor C stocks due to pH-driven shifts in community structure.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

LaeA-Regulated Fungal Traits Mediate Bacterial Community Assembly

Cheese rinds are economically important microbial communities where fungi can impact food quality and aesthetics. The specific mechanisms by which fungi can regulate bacterial community assembly in cheeses, other fermented foods, and microbiomes in general are largely unknown.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Bacterial and fungal growth on fungal necromass and its diverse components: Shared profiles and divergent constraints revealed by high‐throughput phenotyping

1. While fungal necromass is increasingly recognized as a major source of persistent carbon (C) in soils, the relative functional roles of bacteria and fungi in decomposing necromass are not fully resolved, and the processes that select for necromass decomposer communities from the broader soil microbial community are an emerging area of interest. 2. In this study, we characterized the growth of 52 bacterial and 83 fungal strains isolated from necromass and soil on 22 C substrates, including different necromass phenotypes, fungal cell wall polymers, dimers and monomers. 3. We found that the isolation habitat of the strains used in this experiment (necromass vs. soil) had no effect on the substrates they were able to use. Isolates from both microbial domains were able to grow on different labile carbon substrates, polymers and necromass phenotypes. However, fungal growth was most limited by necromass melanin content, while bacterial growth was more limited by the abundance of cell wall polysaccharides. Additionally, overall differences in substrate use between bacteria and fungi were most pronounced on polymer substrates. 4. Collectively, our results suggest that there is substantial functional overlap in necromass substrate use across microbial domains, but some notable differences in bacterial and fungal utilization of cell wall polymers, which can function as a direct energy source or a means of accessing other compounds within necromass. Future studies assessing bacteria and fungi decomposing necromass together rather than in isolation will help to uncover potential physical and chemical interactions within and between these two domains during the decay of this important source of persistent soil C.

dead fungal biomass↗