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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Magnetically responsive nanocultures for direct microbial assessment in soil environments

Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing now unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover previously unidentified biotherapeutics. We present magnetic nanocultures—a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semipermeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for bioprospecting previously uncultured or unknown microbial species.

Usman, Huda [Department of Chemical Engineering, C↗
DOE OSTI2020

Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation

Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO 2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, here we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (β-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment. IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs’ β-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Draft Genome Sequence of Pedococcus sp. Strain 5OH_020, Isolated from California Grassland Soil

The draft genome sequence of the soil bacterium Pedococcus sp. strain 5OH_020, isolated on a natural cobalamin analog, comprises 4.4 Mbp, with 4,108 protein-coding genes. Its genome encodes cobalamin-dependent enzymes, including methionine synthase and class II ribonucleotide reductase. Taxonomic analysis suggests that it is a novel species within the genus Pedococcus .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Complete Genome Sequences of the Soil Oxalotrophic Bacterium Cupriavidus oxalaticus Strain Ox1 and Its Derived mCherry-Tagged Strain

Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69 Mb, with a GC content of 66.9%. The genome sequence of C. oxalaticus Ox1 contains a complete operon for the degradation and assimilation of oxalate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Metagenomes from Experimental Hydrologic Manipulation of Restored Coastal Plain Wetland Soils (Tyrell County, North Carolina)

ABSTRACT Hydrologic changes modify microbial community structure and ecosystem functions, especially in wetland systems. Here, we present 24 metagenomes from a coastal freshwater wetland experiment in which we manipulated hydrologic conditions and plant presence. These wetland soil metagenomes will deepen our understanding of how hydrology and vegetation influence microbial functional diversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Codes for "Shallow Soil Response to a Buried Chemical Explosion with Geophones and Distributed Acoustic Sensing" DAG - 01101646

The codes reproduce the figures of the manuscript entitled "Shallow Soil Response to a Buried Chemical Explosion with Geophones and Distributed Acoustic Sensing" submitted to Journal of Geophysical Research - Solid Earth. Geophone data and Distributed acoustic sensing (DAS) data recorded during the Phase II of the The Source Physics Experiment (SPE) along a fiber-optic cable offshore were processed to understand the response of the shallow subsurface to an explosion. This Ground-based Nuclear Detonation Detection (GNDD), Low Yield Nuclear Monitoring (LYNM), and Source Physics Experiment (SPE) research was funded by the National Nuclear Security Administration, Defense Nuclear Nonproliferation Research and Development (NNSA DNN R&D).

Viens, Loic↗
DOE OSTI2024

RAIS Generic Soil Background Values

The RAIS offers two approaches to background screening: generic and site-specific. The Generic Background Values tool (https://rais.ornl.gov/tools/bg_search.php) contains generic soil background values for selected metals. These values can be applied to any area across the U.S. Users can compare these values against local background data or supplement an existing background value dataset. Results can be downloaded in .xlsx format.

Dolislager, Fred [Oak Ridge National Laboratory (O↗
DOE OSTI2021

Coupling of regional geophysics and local soil-structure models in the EQSIM fault-to-structure earthquake simulation framework

Accurate understanding and quantification of the risk to critical infrastructure posed by future large earthquakes continues to be a very challenging problem. Earthquake phenomena are quite complex and traditional approaches to predicting ground motions for future earthquake events have historically been empirically based whereby measured ground motion data from historical earthquakes are homogenized into a common data set and the ground motions for future postulated earthquakes are probabilistically derived based on the historical observations. This procedure has recognized significant limitations, principally due to the fact that earthquake ground motions tend to be dictated by the particular earthquake fault rupture and geologic conditions at a given site and are thus very site-specific. Historical earthquakes recorded at different locations are often only marginally representative. There has been strong and increasing interest in utilizing large-scale, physics-based regional simulations to advance the ability to accurately predict ground motions and associated infrastructure response. However, the computational requirements for simulations at frequencies of engineering interest have proven a major barrier to employing regional scale simulations. In a U.S. Department of Energy Exascale Computing Initiative project, the EQSIM application development is underway to create a framework for fault-to-structure simulations. This framework is being prepared to exploit emerging exascale platforms in order to overcome computational limitations. This article presents the essential methodology and computational workflow employed in EQSIM to couple regional-scale geophysics models with local soil-structure models to achieve a fully integrated, complete fault-to-structure simulation framework. Here, the computational workflow, accuracy and performance of the coupling methodology are illustrated through example fault-to-structure simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Implementation of stacked ensemble machine learning for the detection of surrogate plutonium contamination in soil via LIBS

Supervised machine learning methods have demonstrated increased utility for the quantification of lanthanide and actinide elements in atomic spectroscopy applications. This study implements laser-induced breakdown spectroscopy (LIBS) for the identification of plutonium surrogate material (CeO 2 ) in soil matrices by training supervised machine learning methods on the recorded spectral data. A bagged ensemble using Random Forest yields the highest sensitivity predictions with a detection limit of 0.015 wt.% CeO 2 . However, high precision in Ce content prediction required the use of a stacked ensemble regression, which provided the superlative Ce quantification model with an error of 0.107% and a detection limit of 0.022 wt.%. Furthermore, the high performance of the stacked ensemble demonstrates its potential to enhance the accuracy and sensitivity of nuclear contaminant detection using field-deployable spectroscopic analyzers in real-world scenarios.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

The ectomycorrhizal fungal symbiont Cenococcum geophilum is of high interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors. C . geophilum is only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within nearly morphologically identical strains. Alternatively, C . geophilum may represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229 C . geophilum isolates from soils under Populus trichocarpa at 123 collection sites spanning a ~283 mile north-south transect in Western Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships within C . geophilum , we performed maximum likelihood and Bayesian phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a global phylogenetic analysis of 789 isolates with publicly available data from the United States, Japan, and European countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on a GAPDH phylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between the GAPDH and ITS rRNA gene region phylogenies, combined with additional analyses revealed stark incongruence between the ITS and GAPDH gene regions, consistent with intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved using Maximum Likelihood and Bayesian approaches (at >80% MLBS and >0.90 BPP respectively), with some clades having intra- and intercontinental distributions. Together these data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and the mode and tempo of recombination patterns.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Plant physiology, shrub size, thaw depth and soil water content, Seward Peninsula, Alaska, 2023

Stomatal response to changing irradiance measurements (m curves), CO2 response (ACi) and light response (AQ) curves on common tussock tundra shrub, graminoid and forb species. Data were collected in July 2023 from three sites on the Seward Peninsula, Kougarok Mile 64, Teller Mile 27 and Council. Measurements were made with LI-COR LI-6800 gas exchange systems on 18 species. For samples from Teller and Kougarok, thaw depth, soil moisture content and dGPS locations are also provided for most samples. Canopy height and canopy diameter are provided for shrubs measured at the Teller site. The data package files include data files, metadata files and the complete instrument output for all gas exchange measurements in .csv format, and a pdf describing the experimental protocols. See the related data package NGA508 for foliar trait data (leaf mass per area, leaf nitrogen concentration).The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 15-year research effort (2012-2027) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗