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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

16s Amplicon Analysis of Soil Data for Interactive effects of depth and differential irrigation on soil microbiome composition and functioning

Genomic DNA was isolated from soil and rhizosphere samples using the Zymo Quick-DNA fecal/soil microbe miniprep kit (catalog no. D6010) according to the manufacturer’s instructions (Zymo Research; Irvine, CA) with the modification of eluting in 100 uL elution buffer. Sample concentrations were quantified using the Qubit dsDNA HS assay kit (Thermo Fisher). For rhizosphere samples only, DNA was subsequently purified using Zymo’s ZR-96 DNA Clean & Concentrator kit (catalog no. D4024) to account for low DNA concentrations of these samples. . In each replicate block, there were five drip irrigation treatments (T1 = 100% normal irrigation, T2 = 56.25%, T3 = 37.5%, T4 = 18.75% and T5=no irrigation. On July 20, the strength of the drought treatments was increased: T1 remained at 100%, whereas T2 changed from 75% to 56.25%, T2 changed from 50% to 37.5%, and T4 changed from 25% to 18.75%. Sequencing was performed as described previously (Naylor, Fansler, et al. 2020). Sequences were amplified on the MiSeq platform (Illumina, San Diego, CA) using 16S primers (515F and 806R) specific to the V4 region. Raw sequence data was processed with the pipeline Hundo for amplicon quality control and annotation. Downstream statistical analyses on 16S datasets were performed using the program R and the packages ‘phyloseq’ and ‘vegan’.

Soil microbiome, metatranscriptomics↗
DOE OSTI2022

Metatransciptomic Analysis Data for Interactive effects of depth and differential irrigation on soil microbiome composition and functioning

RNA was collected from soil at different depths and after three different levels of irrigation T1 100% of normal field irrigation, T4: 18.75% or normal irrigation and T5: unirrigated controls. Total RNA was isolated using the Zymo Quick-RNA fecal/soil microbe miniprep (catalog no. R2040), incorporating the DNase I treatment using Zymo’s DNase I kit (catalog no. E1010). To increase the yield of RNA, we modified the manufacturer’s instructions by first doubling the amount of soil per extraction (from 0.25 g to 0.5 g) and by performing extractions in triplicate before pooling separate extractions together. Certain soil samples (largely those from deeper soil layers) had low yield (< 100 ng per extraction) so additional rounds of extraction were performed to obtain sufficient RNA. RNA concentration was assessed using a Qubit RNA HS assay kit (Thermo Fisher) and RNA quality was determined using an Agilent 2100 BioAnalyzer (Agilent; Santa Clara, CA). The resultant RNA samples were then sequenced by GENEWIZ using Illumina technology (GENEWIZ; South Plainfield, NJ). Sequences were then aligned to a soil metagenome previously obtained from the same site using the Burrows-Wheeler aligner (BWA). SAM files were then converted to raw counts using HTSeq.

Soil microbiome, metatranscriptomics↗
DOE OSTI2024

Integrating biological knowledge for mechanistic inference in the host-associated microbiome

Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Real-Time and Rapid Respiratory Response of the Soil Microbiome to Moisture Shifts

Microbial response to changing environmental factors influences the fate of soil organic carbon, and drought has been shown to affect microbial metabolism and respiration. We hypothesized that the access of microbes to different carbon pools in response to dry–rewet events occurs sequentially at different rates. We amended desiccated soils with 13 C-labeled glucose and measured the rates of 12 CO 2 and 13 CO 2 respiration in real time after rewetting. Using these differentiated 12 CO 2 and 13 CO 2 respiration rate soils after rewetting, we were able to deduce when microbes are accessing different pools of carbon. Immediately upon rewetting, respiration of 12 CO 2 occurred first, with negligible 13 CO 2 respiration. Appreciable metabolism and respiration of the added 13 C glucose did not occur until 15 min after rewetting. We conclude that, while all carbon pools are being accessed in the first 9 h after rewetting, the rate and timing at which new and existing carbon pools are being accessed varies. Within this study, using stable isotope-labeled substrates to discern which carbon pools are metabolized first uniquely illustrates how microorganisms access different carbon pools which has implications into understanding how carbon metabolism can further affect climate, carbon sequestration, and soil health.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Functional and genomic diversity of the sorghum phyllosphere microbiome

A collection of 47 bacteria isolated from the mucilage of aerial roots of energy sorghum is available at the Great Lakes Bioenergy Research Center, Michigan State University, Michigan, USA. We enriched bacteria with putative plant-beneficial phenotypes and included information on phenotypic diversity, taxonomy, and whole genome sequences.

agroecosystems↗
NASA NTRS2022

Unlocking the Spacecraft and Human Habitat Microbiome to Enable the Next Generation of Space Exploration

Planetary protection is the discipline that prevents harmful contamination of the solar system during exploration activities. The current international guidelines and NASA policy addressing biological contamination on spacecraft surfaces contains prescriptive guidelines of spore requirements (e.g., 300 spores/m2, 5×105 spores per spacecraft) applicable to spacecraft bound for Mars. To verify these requirements spacecraft engineers sample spacecraft surfaces throughout the assembly, test and launch operations phase of the mission using damp water cotton swabs and polyester wipes. After sampling, the potential biological contamination is enumerated using a series of traditional microbiology techniques to include sonication, heat shocking at 80°C for 15min to select for spores, and growth on tryptic soy agar at 32°C for 72 hours. To enable crewed missions to Mars and robotic exploration of the Ocean Worlds a risk informed decision making / performance-based approach to assess biological contamination offers a promising solution in the trade space. Recognizing the need for a performance-based approach, NASA’s new Planetary Protection policies now incorporate the agility for missions to be able to leverage a performance or prescriptive approach. One of top contenders in the option space is a coupled quantitative, descriptive and functional based approach to be able to assess the quantity, types and capabilities of the biological contamination present on spacecraft surfaces. A tailored, mission by mission assurance case could then be formulated by building an argument around the target body, projected capabilities surrounding the types of organisms their potential for survival and proliferation, and ability to be transported on the target body to contaminate an area of biological interest. A performance-based requirement would then be used to demonstrate the mission’s compliance in protecting the planetary environment safety objectives. This symposium talk will showcase the background and need case for NASA to develop such a capability as well as provide an update on the efforts underway in developing a transparent and responsible performance-based approach to biological contamination assessments on spacecraft surfaces.

Habitat Microbiome↗
DOE OSTI2021

Xanthohumol Microbiome and Signature in Healthy Adults (the XMaS Trial): Safety and Tolerability Results of a Phase I Triple-Masked, Placebo-Controlled Clinical Trial

Scope Xanthohumol, a prenylflavonoid from hops, has been extensively studied preclinically but has undergone limited research in human subjects. A triple-masked, placebo-controlled phase I clinical trial was conducted to examine the safety and tolerability of xanthohumol. Methods and results Thirty healthy volunteers were randomized to 24?mg/day xanthohumol (99.8% pure) or placebo for eight weeks. Comprehensive metabolic panels, complete blood counts, body weight, vital signs, and health-related quality of life questionnaires were assessed every two weeks. Participants were interviewed for adverse events (AEs) throughout the trial. Thirteen of 14 (93%) and 14 of 16 (88%) participants completed the trial in Group A and B respectively. There were no withdrawals due to AEs. There were no clinically relevant, between-group differences in laboratory biomarkers, body weight, vital signs, or health-related quality of life. There were no severe or FDA-defined serious AEs, but non-serious AEs were documented in both Group A (n=42) and Group B (n=58). Conclusion Over an eight-week period, 24 mg daily xanthohumol was safe and well-tolerated by healthy adults.

Langley, Blake↗
DOE OSTI2022

Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production

Abstract Bioenergy production often focuses on the aboveground feedstock production for conversion to fuel and other materials. However, the belowground component is crucial for soil carbon sequestration, greenhouse gas fluxes, and ecosystem function. Roots maximize feedstock production on marginal lands by acquiring soil resources and mediating soil ecosystem processes through interactions with the microbial community. This belowground world is challenging to observe and quantify; however, there are unprecedented opportunities using current methodologies to bring roots, microbes, and soil into focus. These opportunities allow not only breeding for increased feedstock production but breeding for increased soil health and carbon sequestration as well. A recent workshop hosted by the USDOE Bioenergy Research Centers highlighted these challenges and opportunities while creating a roadmap for increased collaboration and data interoperability through standardization of methodologies and data using F.A.I.R. principles. This article provides a background on the need for belowground research in bioenergy cropping systems, a primer on root system properties of major U.S. bioenergy crops, and an overview of the roles of root chemistry, exudation, and microbial interactions on sustainability. Crucially, we outline how to adopt standardized measures and databases to meet the most pressing methodological needs to accelerate root, soil, and microbial research to meet the pressing societal challenges of the century.

09 BIOMASS FUELS↗
DOE OSTI2020

Reducing host DNA contamination in 16S rRNA gene surveys of anthozoan microbiomes using PNA clamps

Efforts to study the microbial communities associated with corals can be limited by inefficiencies in the sequencing process due to high levels of host amplification by universal bacterial 16S rRNA gene primers. Here, we develop an inexpensive peptide nucleic acid (PNA) clamp that binds to a target sequence of host DNA during PCR and blocks amplification. We then test the ability of this PNA clamp to mitigate host contamination and increase overall microbial sequence coverage on samples from three coral species: the gorgonians Eunicea flexuosa and Gorgonia ventalina, and the scleractinian Porites panamensis. The 20-bp PNA clamp was designed using DNA from E. flexuosa. Adding the PNA clamp during PCR increased the percentage of microbial reads in E. flexuosa samples more than 11-fold. Microbial community diversity was similar without- and with-PNA clamps, as were the relative frequencies of the ten most abundant ASVs (amplicon sequence variants), indicating that the clamps successfully blocked host DNA amplification while simultaneously increasing microbial DNA amplification proportionally across the most abundant taxa. The reduction of E. flexuosa DNA correlated with an increase in the abundance of rarer taxa. The clamp also increased the average percentage of microbial reads in another gorgonian, G. ventalina, by 8.6-fold without altering the microbial community beta diversity, and in a distantly related scleractinian coral, P. panamensis, by nearly double. The reduction of host contamination correlated with the number of nucleotide mismatches between the host amplicon and the PNA clamp. The PNA clamp costs as little as $0.48 per sample, making it an efficient and cost-effective solution to increase microbial sequence coverage for high-throughput sequencing of coral microbial communities.

16S rRNA gene sequencing↗