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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities

Here, we investigated overlooked microbes in soil, candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from soil, an approach typically used for the recovery of viral metagenomes. Concentration of these small cells (<0.2 μm) allowed us to identify these organisms as part of the rare soil biosphere and to sample genomes that were absent from non-size-fractionated metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities

Microorganisms frequently colonize surfaces within food production facilities. Detection of Listeria monocytogenes in this setting relies on culture-dependent methods, but the complex dynamics of bacterial interactions within these environments and their impact on pathogen detection remain largely unexplored. To address this challenge, we applied both 16S rRNA and shotgun quasimetagenomic (enriched microbiome) sequencing of swab culture enrichments from five seafood and seven dairy production environments. Utilizing 16S rRNA amplicon sequencing, we observed variability between 355 samples taken from these 12 production facilities and a distinctive microbiome for each environment. With shotgun quasimetagenomic sequencing, we were able to assemble L. monocytogenes metagenome-assembled genomes (MAGs) from 28 of the 32 culture-positive samples. We compared these MAGs to their corresponding whole-genome sequencing assemblies, which resulted in two polyphyletic clades consisting of L. monocytogenes lineages I and II with 13,195 and 25,556 single-nucleotide polymorphism sites, respectively. The remaining four MAGs did not produce sufficient genome coverage. To understand and establish limits for pathogen detection and subtyping using shotgun quasimetagenomics, these same data sets were downsampled in slilico to produce a titration series of abundances of L. monocytogenes and analyzed. Pathogen detection was achieved for all downsampled data sets, even those with only 3× genome coverage. This study contributes to the understanding of microbial diversity within food production environments and presents insights into the level of genome coverage needed in a metagenome sequencing data set to detect, subtype, and source track a foodborne pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Targeted Biomining and Machine Learning Approaches in Critical Minerals Revealed by a Biogeochemical Survey of a Coal Mine Drainage Remediation System

Abandoned coal mine drainage (AMD) remediation systems in Pennsylvania can concentrate critical minerals and materials (CMM) at levels comparable to mining-grade ores. Remediation systems have varying engineering features and are open to the environment, resulting in diverse microbial colonization and seasonal climate influences that may impact CMM speciation. The location of CMMs, the types of bacterial communities tolerant of these pollutant conditions, and the influence of localized climate on CMM rich remediation systems are not well characterized. Through a one-year spatiotemporal survey of biogeochemistry at a remediation system, we have initiated the process to address these questions. Rare Earth Elements (REE) ranged 180-1,200 ppm and greater than 1,500 bacterial ASVs were classified via 16S sequencing. Analyses indicate biogeochemical differences are heavily influenced by engineering features. Additionally, REE precipitants correlate strongly with the elements Al, Cu, Zn, Be, and U. Unearthing these trends has refined our line of inquiry to explore biological mining opportunities more closely with these metals. Furthermore, we created a Machine Learning Model for predicting AMD REE content, with 89% accuracy, using the data from this study and several others. Further training data is required to create a more reputable model. Recently, global research efforts have prioritized modeling work or the use of the few historical surveys to design experiments. Through our data, we challenge this approach, emphasizing the importance of expanding fundamental survey efforts prior to advanced product design and experimentation.

critical minerals↗
DOE OSTI2024

Microbial Reduction of Manganese Oxides From AMD Solids for the Biomining of Critical Minerals / Rare Earth Elements

Abandoned Coal-Mine Drainage (AMD) is a source of critical minerals (CMs) that can be biomined to increase domestic CM production for the growing tech industry while mitigating current AMD hazardous waste. Pennsylvania has ~11,000 abandoned mines, ~500 of which are currently being treated with passive remediation systems (PRS), designed to increase the pH and precipitate AMD waste onsite. Manganese (Mn) that precipitates from AMD waste can co-precipitate with CMs, and the Mn and CMs will accumulate on the PRS solids over the treatment period. This results in high Mn/CM solids that could produce a valuable leachate if resolubilized. Mn reduction and solubilization can occur through microbial driven geochemical changes such as the acidification of the environment, and it is expected that Mn resolubilization will lead to a co-resolubilization of the CMs. Investigation and stimulation of this microbial resolubilization could result in an affordable CM release process that does not require chemical additives into the environment. However the microbial mechanisms that contribute to Mn resolubilization are poorly understood. Here, we have isolated bacteria capable of resolubilizing Mn from AMD PRS. Five of the bacteria isolates have been identified as Bacillus spp. and two as Corynebacterium spp. that ferment glucose to reduce/solubilize Mn MnO2 by acidogenesis. The bacterial isolates are also capable of solubilizing Mn and CMs (Y, Zr, Sb, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu) from AMD PRS precipitated solids through their production of organic acids. Determining the microbial metabolism and genes involved in the resolubilization of manganese is crucial to optimize the biomining of CMs from AMD solid precipitants. This work addresses the growing need to develop novel CM recovery methods from domestic sources.

critical minerals↗
DOE OSTI2025

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

The Permian Basin is the highest producing oil and gas 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 unique geochemical signal indicating the presence of frac hits in the Permian Basin. We returned to this area with the overall goal of expanding our understanding of the microbial and geochemical dynamics 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 with the rest being novel. For each sample, we measured the pH, alkalinity, geochemical composition, microbial load (qPCR), and microbial community composition (16S rRNA sequencing). 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 in this region. Due to the year-long recovery window between sample collection periods, we anticipate that all of our data will be characterized by the typical high sulfate, low TDS concentrations.

environmental microbiology↗
DOE OSTI2020

Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data

In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each ‘omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA

Abstract Saline springs within the Illinois Basin result from the discharge of deep‐seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%–94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Agnostic capture of pathogens for the detection and diagnostics of emerging threats

The continued emergence of pathogens, whether novel, re-emerging, or engineered, poses a persistent global biosecurity and public health challenge. Recent outbreaks, including COVID-19, Lassa fever, Marburg virus, mpox, and avian influenza, underscore the urgent need for robust systems that enable rapid surveillance, early diagnosis, and timely countermeasures before widespread human transmission occurs. In this article, we focus on early detection technologies and systematically evaluate current diagnostic and sensing modalities. We highlight sequencing and spectroscopy as two complementary approaches capable of providing broad, agnostic detection and rich biological insight. Our analysis emphasizes that scientific innovation alone is insufficient: effective preparedness also requires improved data curation, integration, and sharing to build AI-ready resources that accelerate future responses. We argue for coordinated advances in both technological capabilities and supporting infrastructure to enable the rapid identification and characterization of emerging pathogens and to fully leverage modern science against evolving infectious threats.

Environmental health↗
DOE OSTI2022

Summer thaw duration is a strong predictor of the soil microbiome and its response to permafrost thaw in arctic tundra

Abstract Climate warming has increased permafrost thaw in arctic tundra and extended the duration of annual thaw (number of thaw days in summer) along soil profiles. Predicting the microbial response to permafrost thaw depends largely on knowing how increased thaw duration affects the composition of the soil microbiome. Here, we determined soil microbiome composition from the annually thawed surface active layer down through permafrost from two tundra types at each of three sites on the North Slope of Alaska, USA. Variations in soil microbial taxa were found between sites up to ~90 km apart, between tundra types, and between soil depths. Microbiome differences at a site were greatest across transitions from thawed to permafrost depths. Results from correlation analysis based on multi‐decadal thaw surveys show that differences in thaw duration by depth were significantly, positively correlated with the abundance of dominant taxa in the active layer and negatively correlated with dominant taxa in the permafrost. Microbiome composition within the transition zone was statistically similar to that in the permafrost, indicating that recent decades of intermittent thaw have not yet induced a shift from permafrost to active‐layer microbes. We suggest that thaw duration rather than thaw frequency has a greater impact on the composition of microbial taxa within arctic soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Microbial Functional Responses Explain Alpine Soil Carbon Fluxes under Future Climate Scenarios

Soil microorganisms are sensitive to temperature in cold ecosystems, but it remains unclear how microbial responses are modulated by other important climate drivers, such as precipitation changes. Here, we examine the effects of six in situ warming and/or precipitation treatments in alpine grasslands on microbial communities, plants, and soil carbon fluxes. These treatments differentially affected soil carbon fluxes, gross primary production, and microbial communities. Variations of soil CO 2 and CH 4 fluxes across all sites significantly (r > 0.70, P < 0.050) correlated with relevant microbial functional abundances but not bacterial or fungal abundances. Given tight linkages between microbial functional traits and ecosystem functionality, we conclude that future soil carbon fluxes in alpine grasslands can be predicted by microbial carbon-degrading capacities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Data from TropiRoot 1.0 database: tropical root characteristics across environments

TropiRoot 1.0 is a new tropical root database with root characteristics across environment gradients. It has data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 includes root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology and root chemistry. This initiative represents an approximately 30% increase in the currently available data for tropical roots in the Fine Root Ecology Database (FRED). TropiRoot 1.0, contains root characteristics from 25 different countries where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data was available, including soil data, these data was either extracted and included in the database or their availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match the ones reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions, and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Microbiome to Function: Next Generation Eco-Microbiology Workshop Report

The Biological and Environmental Research (BER) program champions the predictive understanding of complex biological systems to enable energy and infrastructure security. To support this challenging endeavor, BER began funding Science Focus Area (SFA) projects at the national labs a decade ago in order to foster scientific advances that are more easily achieved by sustained team research. BER has recently encouraged collaboration among SFAs as a means to accelerate innovation and scientific impact. To facilitate BER’s vision, the Bioscience Division at Los Alamos National Laboratory (LANL) proposed an annual pan-SFA workshop that would rotate among the National Labs. LANL hosted the first workshop in September 2019 to explore a common challenge—understanding how microbiomes function—and to promote collaboration opportunities among SFAs in BER’s Microbial Genomics Program. The workshop comprised overview presentations of the eight SFAs and two SFA pilots and discussions of near- and midterm opportunities to foster collaboration. These opportunities include 1) sharing isolates, 2) sharing data and storage, 3) establishing common standards and best practices, and 4) fostering scientific exchanges.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Characterization of prokaryotic communities in Puerto Rican caves using 16S rDNA amplicon sequencing

The cave ecosystems host microbial communities adapted to extreme environments. This study utilized 16S rDNA to investigate the prokaryotic diversity across seven caves in Puerto Rico’s northern limestone karst belt. Microbial profiling revealed distinct subterranean communities, enhancing our understanding of cave microbiology and potential applications in environmental conservation and microbial research.

16S↗
DOE OSTI2022

Life cycle assessment of the wood pallet repair and remanufacturing sector in the United States

Wood pallets are ubiquitous products that can be recovered and reused to enhance their service life and environmental performance. Repair/remanufacturing has an important role in extending the service life of the wood pallet. To quantify environmental performances of wood pallet reuse, this study developed representative life cycle inventory data for pallet repair/remanufacturing in the United States based on comprehensive industry-wide production data for 2018. A gate-to-gate life cycle assessment covering raw material supply, raw material transportation and pallet repair/remanufacturing showed that repair/remanufacturing often had the highest impacts, including primary energy consumption at 5.09 MJ and global warming impact at 0.355 kg CO 2 eq per repaired/remanufactured pallet. Electricity consumed onsite followed by nail input and the fuel used by forklifts during the manufacturing drove much of the impacts on the environment. Finally, the results of this study provide valuable information on the repair/remanufacturing impacts, allowing quantification and evaluation of the recovery stage on the overall environmental performance of wood pallets.

09 BIOMASS FUELS↗