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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Metagenome-assembled genomes from East River floodplain sediments near Crested Butte, CO, USA (May to September 2018)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here, we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken in 2018 in May (flooded conditions) and September (drained conditions) at two locations (MCB1 and MCB3) near the Meander C/Pumphouse floodplain sites of the East River. Sediment cores were collected from 2 depths, a near-surface, generally unsaturated depth (30-40 centimeter (cm) depth below surface) and a deeper depth influenced by flooding with redoximorphic features (70-80 cm depth below surface). Sediments were homogenized from the 10 cm core for microbial analyses. A total of 24 metagenomes were sequenced through the Joint genome institute (JGI) corresponding to 8 samples sequenced in triplicate. These metagenomes can be found under Genomes Online Database (GOLD) sequencing project: Gs0141020. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 478 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Metagenome-assembled genomes from East River floodplain sediments near Crested Butte, CO, USA (June to September 2017)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here, we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken in 2017 in June (flooded conditions) and September (drained conditions) at two locations (MCB1 and MCB3) in an active meander (Meander C) of the East River. Sediment cores were collected from 2 depths, a near-surface, generally unsaturated depth (15-40 centimeter (cm) depth below surface) and a deeper depth influenced by flooding with redoximorphic features (50-88 cm depth below surface). Sediments were homogenized from the ~10 cm cores for microbial analyses. A total of 24 metagenomes were sequenced through the Joint genome institute (JGI) corresponding to 8 samples sequenced in triplicate. These metagenomes can be found under Genomes Online Database (GOLD) sequencing project: Gs0151851. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 405 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Organic molecules are deterministically assembled in variably inundated river sediments, but drivers remain unclear

Dissolved organic matter (DOM) is central to ecosystem function. A fundamental challenge is understanding the processes leading to variation in the chemistry of organic molecules that comprise DOM. Here we study these processes in variably inundated riverbed sediments, as an understudied, yet ubiquitous component of rivers. Using null-model approaches adopted from community ecology, we found that within-site variation in environmental conditions caused non-random (i.e., deterministic) shifts in DOM chemistry. Deterministic shifts were observed across diverse biomes, though the strength of determinism varied substantially. We found that the strength of determinism decreased with increasing sediment moisture, but in the form of a constraint space. Many systems fell below the upper constraint boundary, however. We propose a conceptual model based on our results and other publications in which DOM assemblages are hypothesized to be increasingly deterministic across the continuum from the river water column to saturated sediment pore spaces to unsaturated and dry soils/sediments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Metagenome-assembled genomes provide insight into the metabolic potential during early production of Hydraulic Fracturing Test Site 2 in the Delaware Basin

Demand for natural gas continues to climb in the United States, having reached a record monthly high of 104.9 billion cubic feet per day (Bcf/d) in November 2023. Hydraulic fracturing, a technique used to extract natural gas and oil from deep underground reservoirs, involves injecting large volumes of fluid, proppant, and chemical additives into shale units. This is followed by a “shut-in” period, during which the fracture fluid remains pressurized in the well for several weeks. The microbial processes that occur within the reservoir during this shut-in period are not well understood; yet, these reactions may significantly impact the structural integrity and overall recovery of oil and gas from the well. To shed light on this critical phase, we conducted an analysis of both pre-shut-in material alongside production fluid collected throughout the initial production phase at the Hydraulic Fracturing Test Site 2 (HFTS 2) located in the prolific Wolfcamp formation within the Permian Delaware Basin of west Texas, USA. Specifically, we aimed to assess the microbial ecology and functional potential of the microbial community during this crucial time frame. Prior analysis of 16S rRNA sequencing data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. Here, we performed a metagenomic analysis of produced water sampled on Day 33 of production. This analysis yielded three high-quality metagenome-assembled genomes (MAGs), one of which was a Clostridia draft genome closely related to the recently classified Petromonas tenebris. This draft genome likely represents the dominant Clostridia species observed in our 16S rRNA profile. Annotation of the MAGs revealed the presence of genes involved in critical metabolic processes, including thiosulfate reduction, mixed acid fermentation, and biofilm formation. These findings suggest that this microbial community has the potential to contribute to well souring, biocorrosion, and biofouling within the reservoir. Our research provides unique insights into the early stages of production in one of the most prolific unconventional plays in the United States, with important implications for well management and energy recovery.

natural gas↗
NASA NTRS1990

Biospheres and solar system exploration

The implications of biosphere technology is briefly examined. The exploration status and prospects of each world in the solar system is briefly reviewed, including the asteroid belt, the moon, and comets. Five program elements are listed as particularly critical for future interplanetary operations during the coming extraterrestrial century. They include the following: (1) a highway to Space (earth orbits); (2) Orbital Spaceports to support spacecraft assembly, storage, repair, maintenance, refueling, launch, and recovery; (3) a Bridge Between Worlds to transport cargo and crews to the moon and beyond to Mars; (4) Prospecting and Resource Utilization Systems to map and characterize the resources of planets, moons, and asteroids; and (5) Closed Ecology Biospheres. The progress in these five field is reviewed.

Paine, Thomas O.↗
DOE OSTI2025

Metagenome-assembled genomes from Wind River Basin floodplain sediments Riverton, Wyoming site (June to October 2019)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken at three time points from June 12, 2019 to October 23,2019 at a location (PTT1) close to DOE Legacy Management well 855 at the Riverton, Wyoming floodplain site in the Wind River Basin (WRB). The groundwater at this site exhibits persistent U, Mo, and sulfate plumes and is one of the field sites in focus for the SLAC Groundwater Quality SFA program. Sediment samples were collected from 60 to 180 cm below surface every 30cm for microbial analyses through metagenomic sequencing. 15 metagenomes were sequenced through JGI and can be found under Gold sequencing project: Gs0131241. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 780 MAG fasta files and a csv file with quality, taxonomic classification (GTDB RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type. A sample metadata file (samples.csv) that contains site information has also been included.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A scaffolded and annotated reference genome of giant kelp (Macrocystis pyrifera)

Abstract Macrocystis pyrifera (giant kelp), is a brown macroalga of great ecological importance as a primary producer and structure-forming foundational species that provides habitat for hundreds of species. It has many commercial uses (e.g. source of alginate, fertilizer, cosmetics, feedstock). One of the limitations to exploiting giant kelp’s economic potential and assisting in giant kelp conservation efforts is a lack of genomic tools like a high quality, contiguous reference genome with accurate gene annotations. Reference genomes attempt to capture the complete genomic sequence of an individual or species, and importantly provide a universal structure for comparison across a multitude of genetic experiments, both within and between species. We assembled the giant kelp genome of a haploid female gametophyte de novo using PacBio reads, then ordered contigs into chromosome level scaffolds using Hi-C. We found the giant kelp genome to be 537 MB, with a total of 35 scaffolds and 188 contigs. The assembly N50 is 13,669,674 with GC content of 50.37%. We assessed the genome completeness using BUSCO, and found giant kelp contained 94% of the BUSCO genes from the stramenopile clade. Annotation of the giant kelp genome revealed 25,919 genes. Additionally, we present genetic variation data based on 48 diploid giant kelp sporophytes from three different Southern California populations that confirms the population structure found in other studies of these populations. This work resulted in a high-quality giant kelp genome that greatly increases the genetic knowledge of this ecologically and economically vital species.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota

Abstract The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Soil microbiome engineering for sustainability in a changing environment

Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth’s soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

ShadeLab/PAPER_Howe_2023_switchgrass_MetaT

The raw data (metagenomes and metatranscriptomes) for this study are available in the Joint Genomes Institute Genome Portal (https://genome.jgi.doe.gov/portal/ Project ID 503249) with projects designated by year and product type. The MAG genomes analyzed in this paper are available on NCBI, as bioproject PRJNA800073. Plants and microorganisms form beneficial associations. Understanding plant-microbe interactions will inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on field-grown switchgrass and miscanthus and to quantify their activities for switchgrass over two growing seasons. We integrate metagenome and metatranscriptome sequencing from 192 leaf samples collected over representative time points in crop phenology. We curated 40 medium- and high-quality metagenome-assembled-genomes (MAGs) and focused analysis on seasonal transcript recruitment to them. Classes represented by these focal MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) were active and had increases in transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase in the late season. The majority of MAGs had activated stress-associated pathways, including trehalose metabolism, indole acetic acid degradation, betaine biosynthesis, and reactive oxygen species degradation, suggesting direct engagement with the host environment. We also detected seasonally activated biosynthetic pathways for terpenes (carotenoids and isoprenoids) and for various non-ribosomal peptide pathways that were poorly annotated. Overall, this study overcame laboratory and bioinformatic challenges associated with field-based leaf metatranscriptome analysis to inform both general and likely specialized activities of these phyllosphere populations. These activities collectively support that leaf-associated bacterial populations are seasonally dynamic, responsive to host cues, and interactively engage in feedback with the plant. This analysis represented quality filtering of metagenomes and metatranscriptomes (data-preparation folder), metagenome assemblies (metagenome-assembly folder) and metagenome-assembled genome binning, curation, refinement, annotation (mag-evaluation folder). Abundances of sequencing libraries were calculated based on reads mapped (mapping folder). Additionallly, analysis of our annotated results are also included (analysis folder).

Howe, Adina↗
DOE OSTI2023

Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography

Abstract Wetlands store 20–30% of the world’s soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.

Environmental Sciences & Ecology↗
NASA NTRS2022

Using airborne and DESIS imaging spectroscopy to map plant diversity across the largest contiguous tract of tallgrass prairie on earth

Grassland ecosystems are under threat globally, primarily due to land-use and land-cover changes that have adversely affected their biodiversity. Given the negative ecological impacts of biodiversity loss in grasslands, there is an urgent need for developing an operational biodiversity monitoring system that functions in these ecosystems. In this paper, we assessed the capability of airborne and spaceborne imaging spectroscopy (also known as hyperspectral imaging) to capture plant α-diversity in a large naturally-assembled grassland while considering the impact of common management practices, specifically prescribed fire. We collected a robust in-situ plant diversity data set, including species composition and percent cover from 2500 sampling points with different burn ages, from recently-burned to transitional and pre-prescribed fire at the Joseph H. Williams Tallgrass Prairie Preserve in Oklahoma, USA. We expressed in-situ plant α-diversity using the first three Hill numbers, including species richness (number of observed species in a plant community), exponential Shannon entropy index (hereafter Shannon diversity; effective number of common species, where species are weighed proportional to their percent cover), and inverse Simpson concentration index (hereafter Simpson diversity; effective number of dominant species, where more weight is given to dominant species) at four different plot sizes, including 60 m × 60 m, 120 m × 120 m, 180 m × 180 m, and 240 m × 240 m. We collected full-range airborne hyperspectral data with fine spatial resolution (1 m) and visible and near-infrared spaceborne hyperspectral data from DESIS sensor with coarse spatial resolution (30 m), and used the spectral diversity hypothesis—i.e., that the variability in spectral data is largely driven by plant diversity—to estimate α-diversity remotely. In recently-burned plots and those at the transitional stage, both airborne and spaceborne data were capable of capturing Simpson diversity—a metric that calculates the effective number of dominant species by emphasizing abundant species and discounting rare species—but not species richness or Shannon diversity. Further, neither airborne nor spaceborne hyperspectral data sets were capable of capturing plant α-diversity of 60 m × 60 m or 120 m × 120 m plots. Based on these results, three main findings emerged: (1) management practices influence grassland biodiversity patterns that can be remotely detected, (2) both fine- and coarse-resolution remotely-sensed data can detect the effective number of dominant species (e.g., Simpson diversity), and (3) attention should be given to site-specific plant diversity field data collection to appropriately interpret remote sensing results. Findings of this study indicate the feasibility of estimating Simpson diversity in naturally-assembled grasslands using forthcoming spaceborne imagers such as National Aeronautics and Space Administration's Surface Biology and Geology mission.

Hamed Gholizadeh↗
DOE OSTI2025

Site and endmember spectra of terrestrial vegetation and soils for the Colorado Headwaters Ecological Spectroscopy Study, June-July 2025

This dataset provides site and endmember spectra collected during the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS) campaign. The site spectra were collected to help validate airborne hyperspectral data acquired by the National Ecological Observatory Network's aerial observation platform (NEON AOP). Endmember spectra were collected to augment existing spectral libraries with additional samples of bare surfaces and non-photosynthetic vegetation. All measurements were acquired with an Analytical Spectral Devices (ASD) FieldSpec4 Hi-Res NG (Next Generation) spectroradiometer, which records radiance at 1nm (nanometer) intervals from the ultraviolet to the short-wave infrared (350-2500 nm). The dataset includes spectra measured at meadow sites where the CHESS team also collected vegetation samples for trait analyses. The site spectra were collected with the ASD FieldSpec4 palm grip attachment using an 8° field-of-view foreoptic. Site spectra are integrated measurements of the entire surface within the foreoptic’s field of view. For site-level spectra, the sun is the illumination source. A Spectralon panel mounted on a tripod was used for instrument optimization and white reference measurements for all site spectra. Site spectra were acquired within two hours of solar noon and within 48 hours of a NEON AOP overflight. Site spectra are labeled by date, sampling area, and site number according to the naming conventions of the CHESS campaign’s data management plan. The dataset also contains endmember spectra in the following categories: photosynthetic vegetation (PV), non-photosynthetic vegetation (NPV), bare (soil/rock), and flowers. Endmember measurements were acquired using either the contact probe or the leaf clip attachments of the ASD FieldSpec4. In these configurations, the bulb inside the spectrometer provides the light source for the measurements. The spectrometer was optimized and white reference measurements were recorded using the circular white pucks attached to the contact probe and leaf clip. Because they do not rely on solar illumination, contact probe and leaf clip measurements were collected during a broader time frame than the palm grip site spectra. Some endmembers were measured at CHESS meadow sites, while others were collected within the larger sampling area or in nearby locations (e.g. Gothic Townsite) with similar characteristics. Radiance, reflectance, and metadata files are split into three subfolders according to measurement type: proximal/palm grip (prx), contact probe (cp), and leaf clip (lc). Radiance spectra are provided in ASD file format (.asd file extension). All ASD files can be opened using the provided scripts. Metadata is provided in two formats: CSV file format (no geolocation) and GEOJSON file format (includes geolocation for each spectra). The dataset includes a set of pre-processed reflectance spectra as CSV files (yyyymmdd_rfl.csv). The python scripts and jupyter notebook used to calculate reflectance spectra from the ASD radiance data is included here and was previously published at: https://doi.org/10.3334/ORNLDAAC/2446. There is also a folder of JPEG photographs corresponding to selected spectra. We include a protocol document with detailed steps for ASD FieldSpec4 assembly and operations. This data additionally contains a file level metadata (flmd.csv) and data dictionary (dd.csv) file. Geospatial information: Geospatial data for mapping measurement site locations are in the files CHESS_polygons_lai_UTM.geojson, CHESS_polygons_shrub_UTM.geojson, and CHESS_polygons_meadow_UTM.geojson in the companion geospatial package for the 2025 CHESS campaign, ‘CHESS 2025: Location data for field observations and sampling’ (Henderson et al., 2026). CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgment: This research was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration (80NM0018D0004) and was funded by EMIT Extended Mission Phase E Science.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2022

Insight into co-hosts of nitrate reduction genes and antibiotic resistance genes in an urban river of the qinghai-tibet plateau

Microbial co-hosts of nitrate reduction genes (NRGs) and antibiotic resistance genes (ARGs) have been recently reported, but their ecology and biochemical role in urban waterways remain largely unknown. Here, we collected 69 surface water and sediment samples in the Huangshui River on the Qinghai-Tibet Plateau during the wet and dry season associated with comparatively low and high antibiotic levels. Using metagenomic sequencing, we retrieved 278 medium-to-high-quality metagenome-assembled genomes (MAGs) of NRG-ARG co-hosts, mainly belonging to the phyla Proteobacteria, Actinobacteriota, and Bacteroidota. Of microorganisms carrying ARGs, a high proportion (75.3?94.9%) also encoded NRGs, supporting nitrate reducing bacteria as dominant hosts of ARGs. Seasonal changes in antibiotic levels corresponded to significant variation in the relative abundance and community composition of NRG-ARG co-host in both water and sediments, resulting in a concomitant change in antibiotic resistance pathways. In contrast, the contribution of NRG-ARG co-hosts to nitrate reduction was stable between seasons. Further, we identify specific antibiotics (e.g., sulphonamides) and microbial taxa (e.g., Acinetobacter and Hafnia) that may disproportionately impact these relationships to serve as a basis for laboratory investigations into bioremediation strategies. Our study suggests that highly abundant nitrate reducing microorganisms in contaminated environments may also directly impact human health as carriers of antibiotic resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Anti-fungal bioactive terpenoids in the bioenergy crop switchgrass (Panicum virgatum) may contribute to ecotype-specific microbiome composition

Abstract Plant derived bioactive small molecules have attracted attention of scientists across fundamental and applied scientific disciplines. We seek to understand the influence of these phytochemicals on rhizosphere and root-associated fungi. We hypothesize that – consistent with accumulating evidence that switchgrass genotype impacts microbiome assembly – differential terpenoid accumulation contributes to switchgrass ecotype-specific microbiome composition. An initial in vitro Petri plate-based disc diffusion screen of 18 switchgrass root derived fungal isolates revealed differential responses to upland- and lowland-isolated metabolites. To identify specific fungal growth-modulating metabolites, we tested fractions from root extracts on three ecologically important fungal isolates – Linnemania elongata, Trichoderma sp. and Fusarium sp. Saponins and diterpenoids were identified as the most prominent antifungal metabolites. Finally, analysis of liquid chromatography-purified terpenoids revealed fungal inhibition structure – activity relationships (SAR). Saponin antifungal activity was primarily determined by the number of sugar moieties – saponins glycosylated at a single core position were inhibitory whereas saponins glycosylated at two core positions were inactive. Saponin core hydroxylation and acetylation were also associated with reduced activity. Diterpenoid activity required the presence of an intact furan ring for strong fungal growth inhibition. These results inform future breeding and biotechnology strategies for crop protection with reduced pesticide application.

09 BIOMASS FUELS↗