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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Merging Fungal and Bacterial Community Profiles via an Internal Control

Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. As a result, this IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

MicroFisher: Fungal taxonomic classification for metatranscriptomic and metagenomic data using multiple short hypervariable markers

AbstractProfiling the taxonomic and functional composition of microbes using metagenomic (MG) and metatranscriptomic (MT) sequencing is advancing our understanding of microbial functions. However, the sensitivity and accuracy of microbial classification using genome– or core protein-based approaches, especially the classification of eukaryotic organisms, is limited by the availability of genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel approach that applies multiple hypervariable marker genes to profile fungal communities from MGs and MTs. This approach utilizes the hypervariable regions of ITS and large subunit (LSU) rRNA genes for fungal identification with high sensitivity and resolution. Simultaneously, we propose a computational pipeline (MicroFisher) to optimize and integrate the results from classifications using multiple hypervariable markers. To test the performance of our method, we applied MicroFisher to the synthetic community profiling and found high performance in fungal prediction and abundance estimation. In addition, we also used MGs from forest soil and MTs of root eukaryotic microbes to test our method and the results showed that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. Overall, MicroFisher serves as a novel pipeline for classification of fungal communities from MGs and MTs.

Wang, Haihua↗
DOE OSTI2023

Molecular Transformation and Metabolic Insights of Microbial Electrolysis Treatment and Valorization of Post-hydrothermal Liquefaction Wastewater

Hydrothermal liquefaction (HTL) presents a promising approach for the conversion of wet waste into biocrude and biofuels. However, the post-hydrothermal liquefaction wastewater (PHW) poses significant challenges for treatment and valorization due to its high concentration and complex nature. In this study, we investigated the conversion pathways of major organic contaminants within the microbial electrolytic treatment of PHW from food waste HTL. To achieve this, we employed high-performance liquid chromatography (HPLC) and 2D nuclear magnetic resonance (NMR). Our findings demonstrate volatile fatty acids (VFAs) and monohydric and polyhydric alcohols were effectively transformed through the synergistic metabolism of fermentative and electroactive bacteria, which led to over 70% COD removal of the recalcitrant compounds and a record high H2 production rate (1.62 L L -1 d -1 ). We also employed the liquid-state 15N NMR on wastewater samples for the first time and revealed that the nitrogen-containing heteroaromatics were persistent to microbial electrochemical treatment. By integrating the chemical profiles with bioanode community profiles, we constructed a metabolic network that provides insights for enhancing treatment efficiency and facilitating resource recovery.

08 HYDROGEN↗
DOE OSTI2021

Site and Bioenergy Cropping System Similarly Affect Distinct Live and Total Soil Microbial Communities

Bioenergy crops are a promising energy alternative to fossil fuels. During bioenergy feedstock production, crop inputs shape the composition of soil microbial communities, which in turn influences nutrient cycling and plant productivity. In addition to cropping inputs, site characteristics (e.g., soil texture, climate) influence bacterial and fungal communities. We explored the response of soil microorganisms to bioenergy cropping system (switchgrass vs. maize) and site (sandy loam vs. silty loam) within two long-term experimental research stations. The live and total microbial community membership was investigated using 16S and ITS amplicon sequencing of soil RNA and DNA. For both nucleic acid types, we expected fungi and prokaryotes to be differentially impacted by crop and site due their dissimilar life strategies. We also expected live communities to be more strongly affected by site and crop than the total communities due to a sensitivity to recent stimuli. Instead, we found that prokaryotic and fungal community composition was primarily driven by site with a secondary crop effect, highlighting the importance of soil texture and fertility in shaping both communities. Specific highly abundant prokaryotic and fungal taxa within live communities were indicative of site and cropping systems, providing insight into treatment-specific, agriculturally relevant microbial taxa that were obscured within total community profiles. Within live prokaryote communities, predatory Myxobacteria spp. were largely indicative of silty and switchgrass communities. Within live fungal communities, Glomeromycota spp. were solely indicative of switchgrass soils, while a few very abundant Mortierellomycota spp. were indicative of silty soils. Site and cropping system had distinct effects on the live and total communities reflecting selection forces of plant inputs and environmental conditions over time. Comparisons between RNA and DNA communities uncovered live members obscured within the total community as well as members of the relic DNA pool. The associations between live communities and relic DNA are a product of the intimate relationship between the ephemeral responses of the live community and the accumulation of DNA within necromass that contributes to soil organic matter, and in turn shapes soil microbial dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Carbon dioxide (CO2) flux, amplicon sequencing and liquid chromatography–mass spectrometry (LC-MS) data for pyrogenic organic matter (PYOM) amended soil incubations in lab, Madison, WI, 2021-22

This dataset comprises soil-pyrogenic organic matter (PyOM) incubation experiments conducted in a laboratory setting. The focus was on measuring carbon dioxide (CO2) flux emitted in the headspace of incubation jars over a one-month period. The aim was to estimate carbon mineralization from two different carbon fractions in PyOM, as well as carbon mineralization from soil organic carbon (SOC). Bacterial and fungal community profiles were tracked at various time points during the incubation to observe changes in the overall community and specific responders to PyOM. LC-MS analysis of soil samples was also performed to monitor changes in the soil's chemical composition.The provided dataset includes processed CO2 flux measurements obtained from the Picarro-multiplexer measurement setup for each sample incubation jar. This data is available in the "CO2Flux.csv" file. Additionally, the dataset includes CO2 flux data partitioned to estimate mean carbon mineralization from the two PyOM carbon fractions, bulk PyOM, and SOC. The cumulative carbon mineralization data is provided in "cml_respired.csv," while the rate of carbon mineralization data is in "rate_respired.csv." The file "cml_respired_lastcyc.csv" contains cumulative carbon mineralization data for the PyOM carbon fractions, bulk PyOM, and SOC throughout the entire incubation period.For the LC-MS analysis, the raw data can be found in the "20220721_NZ_PeakHeights_FinalAnalysis.csv" file, while sample metadata is provided in "20220721_NZpilot_Metadata.csv". Processed LC-MS data is available in the file "20220721_NZ_FINAL_msdat_sub3.csv". Lastly, the dataset includes the relative abundance data for bacterial genera that exhibited a significant positive response to the addition of PyOM produced at 350 degrees Celsius, which can be found in "resp_genera_350.csv".

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Impact of intense sanitization procedures on bacterial communities recovered from floor drains in pork processing plants

Pork processing plants in the United States (US) cease operations for 24–48 h every six or twelve months to perform intense sanitization (IS) using fogging, foaming, and further antimicrobial treatments to disrupt natural biofilms that may harbor pathogens and spoilage organisms. The impact such treatments have on short-term changes in environmental microorganisms is not well understood, nor is the rate at which bacterial communities return. Swab samples were collected from floor drains to provide representative environmental microorganisms at two US pork processing plants before, during, and after an IS procedure. Samples were collected from four coolers where finished carcasses were chilled and from four locations near cutting tables. Each sample was characterized by total mesophile count (TMC), total psychrophile count (TPC), and other indicator bacteria; their biofilm-forming ability, tolerance of the formed biofilm to a quaternary ammonium compound (300 ppm, QAC), and ability to protect co-inoculated Salmonella enterica. In addition, bacterial community composition was determined using shotgun metagenomic sequencing. IS procedures disrupted bacteria present but to different extents depending on the plant and the area of the plant. IS reduced TPC and TMC, by up to 1.5 Log 10 CFU only to return to pre-IS levels within 2–3 days. The impact of IS on microorganisms in coolers was varied, with reductions of 2–4 Log 10 , and required 2 to 4 weeks to return to pre-IS levels. The results near fabrication lines were mixed, with little to no significant changes at one plant, while at the other, two processing lines showed 4 to 6 Log 10 reductions. Resistance to QAC and the protection of Salmonella by the biofilms varied between plants and between areas of the plants as well. Community profiling of bacteria at the genus level showed that IS reduced species diversity and the disruption led to new community compositions that in some cases did not return to the pre-IS state even after 15 to 16 weeks. The results found here reveal the impact of using IS to disrupt the presence of pathogen or spoilage microorganisms in US pork processing facilities may not have the intended effect.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Inclusive Shared Solar: The State Policy Landscape and Select Community Solar Project Profiles

This report provides an overview of the LMI community solar landscape to help State Energy Offices, LIHEAP offices, and other key stakeholders understand and take advantage of opportunities to expand the reach and impact of community solar programs. It discusses common LMI community solar policy and program considerations and profiles four projects in three different states to show how state policy decisions can impact community solar program design and implementation.

14 SOLAR ENERGY↗
DOE OSTI2025

Community-Centric Microgrid Feasibility Analysis Framework to Accelerate Resilience of Island Communities

Marine energy offers a reliable energy solution for island and coastal communities, which often lack traditional local generation, to support their transition to energy independence and reduce reliance on externally imported fuels. Successful deployment of new technologies in these isolated locations requires community acceptance and approval from the outset, as these communities typically lack the financial and technical resources to operate and maintain new systems. This report presents a community-centric microgrid planning framework for remote coastal and island communities. Community engagement is integrated as the first step in the planning process, incorporating community profiles and visions into energy development scenarios. A case study was conducted in St. George, Pribilof Islands, Alaska, which relies entirely on diesel yet has significant wind and wave energy potential. Community engagement revealed a unique history and current economic status, with an interest in adopting advanced energy technologies despite past failures. Various microgrid configurations were optimized, considering different technologies to meet current and future energy needs while balancing cost and energy resilience. Wave energy converters (WECs) were a key component, integrated with other energy sources using the Xendee optimization tool. The Marine Energy Microgrid Toolkit, developed as part of this work, uses commercial power system analysis tools to optimize and analyze microgrid scenarios. The developed framework and toolkit can be applied to island and coastal communities to enhance resilience and support microgrid deployments. Future enhancements will include incorporating new marine resources, developing dynamic models, and automating the integration of Xendee and PowerFactory simulations.

02 PETROLEUM↗
NASA NTRS2003

Community-level physiological profiling performed with an oxygen-sensitive fluorophore in a microtiter plate

Community-level physiological profiling based upon fluorometric detection of oxygen consumption was performed on hydroponic rhizosphere and salt marsh litter samples by using substrate levels as low as 50 ppm with incubation times between 5 and 24 h. The rate and extent of response were increased in samples acclimated to specific substrates and were reduced by limiting nitrogen availability in the wells.

NASA Discipline Life Support Systems↗
DOE OSTI2021

Cometabolic Vinyl Chloride Degradation at Acidic pH Catalyzed by Acidophilic Methanotrophs Isolated from Alpine Peat Bogs

Remediation of toxic chlorinated ethenes via microbial reductive dechlorination can lead to ethene formation; however, the process stalls in acidic groundwater, leading to the accumulation of carcinogenic vinyl chloride (VC). This study explored the feasibility of cometabolic VC degradation by moderately acidophilic methanotrophs. Furthermore, two novel isolates, Methylomonas sp. strain JS1 and Methylocystis sp. strain MJC1, were obtained from distinct alpine peat bogs located in South Korea. Both isolates cometabolized VC with CH 4 as the primary substrate under oxic conditions at pH at or below 5.5. VC cometabolism in axenic cultures occurred in the presence (10 μM) or absence (<0.01 μM) of copper, suggesting that VC removal had little dependence on copper availability, which regulates expression and activity of soluble and particulate methane monooxygenases in methanotrophs. The model neutrophilic methanotroph Methylosinus trichosporium strain OB3b also grew and cometabolized VC at pH 5.0 regardless of copper availability. Bioaugmentation of acidic peat soil slurries with methanotroph isolates demonstrated enhanced VC degradation and VC consumption below the maximum concentration level of 2 μg L –1 . Community profiling of the microcosms suggested species-specific differences, indicating that robust bioaugmentation with methanotroph cultures requires further research.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Geobacter sp. Strain IAE Dihaloeliminates 1,1,2-Trichloroethane and 1,2-Dichloroethane

We report that chlorinated ethanes, including 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA), are widespread groundwater contaminants. Enrichment cultures XR DCA and XR TCA derived from river sediment dihaloeliminated 1,2-DCA to ethene and 1,1,2-TCA to vinyl chloride (VC), respectively. The XR TCA culture subsequently converted VC to ethene via hydrogenolysis. Microbial community profiling demonstrated the enrichment of Geobacter 16S rRNA gene sequences in both the XR DCA and XR TCA cultures, and Dehalococcoides mccartyi (Dhc) sequences were only detected in the ethene-producing XR TCA culture. The presence of a novel Geobacter population, designated as Geobacter sp. strain IAE, was identified by the 16S rRNA gene-targeted polymerase chain reaction and Sanger sequencing. Time-resolved population dynamics attributed the dihaloelimination activity to strain IAE, which attained the growth yields of 0.93 ± 0.06 x 10 7 and 1.18 ± 0.14 x 10 7 cells per μmol Cl -1 released with 1,2-DCA and 1,1,2-TCA as electron acceptors, respectively. In contrast, Dhc growth only occurred during VC-to-ethene hydrogenolysis. Our findings discover a Geobacter sp. strain capable of respiring multiple chlorinated ethanes and demonstrate the involvement of a broader diversity of organohalide-respiring bacteria in the detoxification of 1,2-DCA and 1,1,2-TCA.

1,1,2-trichloroethane↗
DOE OSTI2021

Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation

Mechanisms controlling CO 2 and CH 4 production in wetlands are central to understanding carbon cycling and greenhouse gas exchange. However, the volatility of these respiration products complicates quantifying their rates of production in the field. Attempts to circumvent the challenges through closed system incubations, from which gases cannot escape, have been used to investigate bulk in situ geochemistry. Efforts towards mapping mechanistic linkages between geochemistry and microbiology have raised concern regarding sampling and incubation-induced perturbations. Microorganisms are impacted by oxygen exposure, increased temperatures and accumulation of metabolic products during handling, storage, and incubation. We probed the extent of these perturbations, and their influence on incubation results, using high-resolution geochemical and microbial gene-based community profiling of anaerobically incubated material from three wetland habitats across a permafrost peatland. We compared the original field samples to the material anaerobically incubated over 50 days. Bulk geochemistry and phylum-level microbiota in incubations largely reflected field observations, but divergence between field and incubations occurred in both geochemistry and lineage-level microbial composition when examined at closer resolution. Despite the changes in representative lineages over time, inferred metabolic function with regards to carbon cycling largely reproduced field results suggesting functional consistency. Habitat differences among the source materials remained the largest driver of variation in geochemical and microbial differences among the samples in both incubations and field results. While incubations may have limited usefulness for identifying specific mechanisms, they remain a viable tool for probing bulk-scale questions related to anaerobic C cycling, including CO 2 and CH 4 dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Linking Spatiotemporal Biological Data to Predict Harmful Algal Blooms

Cyanobacterial Harmful Algal Blooms (cHABs) have significant impacts on an affected region’s economy, ecology, and human health. The blooms can release toxins that kill fish and poison water for people and animals. The global adverse effects of cHABs are exacerbated by the consequences of climate change and increased pollution. Though the phenomena are well documented, scientists’ efforts to mitigate the damage are hampered by insufficient predictive models and incomplete granular knowledge of cHAB community structure. With a goal of leveraging bioinformatics and machine learning tools to better understand and predict cHABs, we are first exploring water sample data sets. Using nearly four thousand samples from the National Center for Biotechnology Information Sequence Read Archive (NCBI-SRA) across 16 years with latitude and longitude embedded in the metadata, we mapped the location of the samples onto a Lake Erie shape file. We combined information about location, date, and community taxa in the NCBI samples to discover factors that determine cHAB features. The data are separated into three distinct zones, with the majority pooled at the southwest end of the lake and occurring in 2017. The samples are rich in biological data; our next steps are to carry out whole genome sequence analysis and use the community profiles as part of our predictive machine learning model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Final Report for CSP Tower Public Opinion and Education Project

As part of the CSP Plant Optimization Study for the California Power Market (DE-EE0009809) the project wanted to understand the public’s opinion of the technology and and explore the types of community engagement that is needed to support such development. The initial objectives for the public perception activities were twofold. The primary objective was to gather public opinion and feedback from the communities living near the two operating solar power tower plants, Ivanpah and Crescent Dunes, and to distill lessons learned from the community engagement conducted before, during, and after the plants were developed to inform future development. This included outreach to nearby airports. The other objective was to gauge public opinion about large-scale solar, specifically CSP towers, to start educating the public on the benefits and to begin building relationships with communities of interest, initially targeting the Kingman, Arizona area. The objectives shifted after the first exploratory trip to Ivanpah and Kingman, however, as it became apparent that it would be challenging to gather public opinion from the community surrounding Ivanpah that could be useful for other community profiles, and the company wasn’t ready to address the concerns in Kingman. Another area was chosen, therefore, to represent those where future development is possible. The recently published Lawrence Berkeley National Lab Perceptions of Large-Scale Solar Project Neighbors Study exemplified public perception polling based on social science and served as the foundation for the survey questions taken to the field. The intent was to ensure that people knew their input was valued and that the time they spent was valuable for the participant as well. It has been noted in the literature that in-person interaction has greater benefits than activities online or via mail, as well as limits the expense.

14 SOLAR ENERGY↗
NASA NTRS2000

Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (TRFLP) analysis

In this report, we describe an experiment conducted at Kennedy Space Center in the biomass production chamber (BPC) using soybean plants for purification and processing of human hygiene water. Specifically, we tested whether it was possible to detect changes in the root-associated bacterial assemblage of the plants and ultimately to identify the specific microorganism(s) which differed when plants were exposed to hygiene water and other hydroponic media. Plants were grown in hydroponics media corresponding to four different treatments: control (Hoagland's solution), artificial gray water (Hoagland's+surfactant), filtered gray water collected from human subjects on site, and unfiltered gray water. Differences in rhizosphere microbial populations in all experimental treatments were observed when compared to the control treatment using both community level physiological profiles (BIOLOG) and molecular fingerprinting of 16S rRNA genes by terminal restriction fragment length polymorphism analysis (TRFLP). Furthermore, screening of a clonal library of 16S rRNA genes by TRFLP yielded nearly full length SSU genes associated with the various treatments. Most 16S rRNA genes were affiliated with the Klebsiella, Pseudomonas, Variovorax, Burkholderia, Bordetella and Isosphaera groups. This molecular approach demonstrated the ability to rapidly detect and identify microorganisms unique to experimental treatments and provides a means to fingerprint microbial communities in the biosystems being developed at NASA for optimizing advanced life support operations.

NASA Discipline Life Support Systems↗
DOE OSTI2025

Disruption of the endogenous indole glucosinolate pathway impacts the Arabidopsis thaliana root exudation profile and rhizobacterial community

Root exudates are composed of primary and secondary metabolites known to modulate the rhizosphere microbiota. Glucosinolates are defense compounds present in the Brassicaceae family capable of deterring pathogens, herbivores and biotic stressors in the phyllosphere. In addition, traces of glucosinolates and their hydrolyzed byproducts have been found in the soil, suggesting that these secondary metabolites could play a role in the modulation and establishment of the rhizosphere microbial community associated with this family. Here, we used Arabidopsis thaliana mutant lines, including the cyp79B2cyp79B3 double mutant line with a disruption in the indole glucosinolate pathway and atr1D, which overexpresses ATR1 and increases glucosinolate production. These lines were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 16S rRNA amplicon sequencing to evaluate how genetic modifications to the indole glucosinolate pathway affects the root exudate profile of Arabidopsis thaliana, and, in turn, impacts the rhizosphere microbial community. Metabolic analysis of root exudates from the wild-type Columbia (Col-0), along with the mutant lines, confirmed that alterations to the indole glucosinolate biosynthetic pathway result in shifts in the root exudate profile of the plant. We observed changes in the relative abundance of exuded metabolites. Moreover, 16S rRNA amplicon sequencing results provided evidence that the rhizobacterial communities associated with the plant lines used were directly impacted in diversity and community composition. Here, this work provides further information on the involvement of secondary metabolites and their role in modulating the rhizobacterial community. Root metabolites dictate the presence of different bacterial species, including plant growth-promoting rhizobacteria (PGPR). Our results suggest that genetic alterations in the indole glucosinolate pathway cause disruptions beyond the endogenous levels of the plant, significantly changing the abundance and presence of different metabolites in the root exudates of the plants as well as the microbial rhizosphere community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone

Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ.

59 BASIC BIOLOGICAL SCIENCES↗