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89 records · Page 5

All sources NASA NTRS DOE OSTI

DOE OSTI2024

Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

$\mathrm{COBRA}$ improves the completeness and contiguity of viral genomes assembled from metagenomes

Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2011

Investigating the Potential Range Expansion of the Vector Mosquito Aedes Aegypti in Mexico with NASA Earth Science Remote Sensing Results

Dengue (Breakbone) fever is caused by one of four viruses carried by mosquitoes in tropical and subtropical areas. Cases have increased dramatically in the past few decades; there are currently approximately 100 million infections annually around the globe. Our project will integrate environmental observations, including weather, land use, vegetation type, amount and greenness, soil moisture, and mosquito populations with investigations of the human dynamics of the system via household surveys.

Estes, Sue M.↗

DOE OSTI2024

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

Biochemistry & Molecular Biology↗

NASA NTRS1999

Biological Sterilization of Returned Mars Samples

Martian rock and soil, collected by robotic spacecraft, will be returned to terrestrial laboratories early in the next century. Current plans call for the samples to be immediately placed into biological containment and tested for signs of present or past life and biological hazards. It is recommended that "Controlled distribution of unsterilized materials from Mars should occur only if rigorous analyses determine that the materials do not constitute a biological hazard. If any portion of the sample is removed from containment prior to completion of these analyses it should first be sterilized." While sterilization of Mars samples may not be required, an acceptable method must be available before the samples are returned to Earth. The sterilization method should be capable of destroying a wide range of organisms with minimal effects on the geologic samples. A variety of biological sterilization techniques and materials are currently in use, including dry heat, high pressure steam, gases, plasmas and ionizing radiation. Gamma radiation is routinely used to inactivate viruses and destroy bacteria in medical research. Many commercial sterilizers use Co-60 , which emits gamma photons of 1.17 and 1.33 MeV. Absorbed doses of approximately 1 Mrad (10(exp 8) ergs/g) destroy most bacteria. This study investigates the effects of lethal doses of Co-60 gamma radiation on materials similar to those anticipated to be returned from Mars. The goals are to determine the gamma dose required to kill microorganisms in rock and soil samples and to determine the effects of gamma sterilization on the samples' isotopic, chemical and physical properties. Additional information is contained in the original extended abstract.

Allen, C. C.↗

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↗

DOE OSTI2021

The Switchgrass Microbiome: A Review of Structure, Function, and Taxonomic Distribution

Switchgrass (Panicum virgatum L.) has been championed as a promising bioenergy crop due to its high productivity across a wide environmental range. The switchgrass microbiome—including bacteria, archaea, fungi, and other microbiota inhabiting soil and plant tissues—can influence plant function substantially. We conducted a review of the literature investigating switchgrass microbiome structure, key functional roles, and taxa isolated from field-grown plants. Although site conditions and plant compartment (i.e., location within shoots, roots, or root-influenced soil) appear to be the strongest drivers of switchgrass microbiome structure, the microbiome is also shaped by climate, season, and host genotype. Studies comparing across plant species show that the switchgrass microbiome is more similar to the microbiomes of other perennial plants than to the microbiomes of annual plants. Members of the switchgrass microbiome confer several benefits to their host. Most notably, mycorrhizal fungi can increase plant biomass many-fold, associative nitrogen-fixing bacteria can provide a substantial portion of the plant’s nitrogen demand, and fungal endophytes can improve plant tolerance to drought. Although the fungi and bacteria cultured from switchgrass represent only a portion of the microbiome, these serve as a valuable resource for researchers interested in investigating functional outcomes of the switchgrass microbiome. We highlight areas where additional research is necessary for a more comprehensive understanding of switchgrass microbiome structure, function, and potential to enhance sustainable bioenergy production. Key gaps include the role of understudied organisms (e.g., viruses, microeukaryotes, and nonmycorrhizal fungi), multitrophic relationships, mechanisms underpinning switchgrass–microbiome interactions, and field-scale validation of experimental findings.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2003

Dust, Climate, and Human Health

Air pollution from both natural and anthropogenic causes is considered to be one of the most serious world-wide environment-related health problems, and is expected to become worse with changes in the global climate. Dust storms from the atmospheric transport of desert soil dust that has been lifted and carried by the winds - often over significant distances - have become an increasingly important emerging air quality issue for many populations. Recent studies have shown that the dust storms can cause significant health impacts from the dust itself as well as the accompanying pollutants, pesticides, metals, salt, plant debris, and other inorganic and organic materials, including viable microorganisms (bacteria, viruses and fungi). For example, thousands of tons of Asian desert sediments, some containing pesticides and herbicides from farming regions, are commonly transported into the Arctic during dust storm events. These chemicals have been identified in animal and human tissues among Arctic indigenous populations. Millions of tons of airborne desert dust are being tracked by satellite imagery, which clearly shows the magnitude as well as the temporal and spatial variability of dust storms across the "dust belt" regions of North Africa, the Middle East, and China. Th~s paper summarizes the most recent findings on the effects of airborne desert dust on human health as well as potential climate influences on dust and health.

Maynard, Nancy G.↗

NASA NTRS2003

Dust, Climate, and Human Health

Air pollution from both natural and anthropogenic causes is considered to be one of the most serious world-wide environment-related health problems, and is expected to become worse with changes in the global climate. Dust storms from the atmospheric transport of desert soil dust that has been lifted and carried by the winds - often over significant distances - have become an increasingly important emerging air quality issue for many populations. Recent studies have shown that the dust storms can cause significant health impacts from the dust itself as well as the accompanying pollutants, pesticides, metals, salt, plant debris, and other inorganic and organic materials, including viable microorganisms (bacteria, viruses and fungi). For example, thousands of tons of Asian desert sediments, some containing pesticides and herbicides from farming regions, are commonly transported into the Arctic during dust storm events. These chemicals have been identified in animal and human tissues among Arctic indigenous populations. Millions of tons of airborne desert dust are being tracked by satellite imagery, which clearly shows the magnitude as well as the temporal and spatial variability of dust storms across the "dust belt" regions of North Africa, the Middle East, and China. This paper summarizes the most recent findings on the effects of airborne desert dust on human health as well as potential climate influences on dust and health.

Maynard, Nancy G.↗

NASA NTRS1974

Utilizing ERTS imagery to detect plant diseases and nutrient deficiencies, soil types and soil moisture levels

The author has identified the following significant results. ERTS-1 imagery may be used to delineate soil associations. It does have the capacity to divide soils into groups such that their land use and management would be similar. It offers definite potential for making grass flood-plain, wetland, river shoreline, and land use change surveys. Production of volume strata and forest type from the two usable bands of ERTS-1 imagery were of questionable value. No imagery was received for evaluation during the time of year when maine dwarf mosaic virus and southern corn leaf blight were active.

Parks, W. L.↗

NASA NTRS1985

Concepts, strategies and potentials using hypo-g and other features of the space environment for commercialization using higher plants

Opportunities for releasing, capturing, constructing and/or fixing the differential expressions or response potentials of the higher plant genome in the hypo-g environment for commercialization are explored. General strategies include improved plant-growing, crop and forestry production systems which conserve soil, water, labor and energy resources, and nutritional partitioning and mobilization of nutrients and synthates. Tissue and cell culture techniques of commercial potential include the growing and manipulation of cultured plant cells in vitro in a bioreactor to produce biologicals and secondary plants of economic value. The facilitation of plant breeding, the cloning of specific pathogen-free materials, the elimination of growing point or apex viruses, and the increase of plant yield are other O-g applications. The space environment may be advantageous in somatic embryogenesis, the culture of alkaloids, and the development of completely new crop plant germ plasm.

Krikorian, A. D.↗

DOE OSTI2025

Increasing Mosquito Abundance Under Global Warming

Mosquitoes are a key virus vector that poses significant health threats globally, affecting 700 million individuals and causing 1 million deaths annually. Accurately predicting mosquito abundance and dispersion remains a challenge. Complex interactions between mosquito dynamics and various environmental factors, notably hydrology, contribute to this challenge. Existing models typically focus on precipitation and temperature and often overlook further impacts of hydrological variables within mosquito modeling. In this study, we developed an artificial intelligence‐based model for mosquito dynamics, explicitly accounting for different hydrological variables, such as precipitation, soil moisture and streamflow. Using Toronto, Canada, as a case study, we identified causal relationships between changes in mosquito populations, hydrological factors, vegetation (e.g., leaf area index), and climate variables (e.g., daylight length, precipitation, and temperature). We embedded these relationships into a Long Short‐Term Memory (LSTM) Neural Network Model capable of accurately detecting mosquito dynamics across annual, seasonal, and monthly time scales. The LSTM is able to explain, on average, approximately 40% of the variance in the observed mosquito abundance data. Using the calibrated model, we predicted that the summer season mosquito abundance would increase by ∼16% and ∼19% under an intermediate greenhouse emission scenario, Shared Socioeconomic Pathway (SSP) 2–4.5, and a high greenhouse emission scenario, SSP5‐8.5, respectively. We expect that this model can serve as a valuable tool and inform science‐based decisions affecting mosquito dynamics and public health. It can also build a foundation for future risk analysis at the regional and larger scales.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

A genomic catalog of Earth’s microbiomes

Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Microbial Community Analysis & Functional Evaluation in Soils

The overall objective of this proposal was to develop technologies to alter the composition and function of important members of microbial communities. In particular, the overall objective of the microbial community editing portion of the proposal focuses on developing foundational tools and understanding required to predict, alter and design grass rhizosphere communities impacting DOE missions. Specifically, the project is centered on the Microbial Community Analysis & Functional Evaluation in Soils (m-CAFES) to manipulate microbial consortia associated with plants of interest for the bioenergy sector, under the presumption that bacterial communities can be manipulated to enhance plant health. For tasks of specific interest to us, we are focusing on developing novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based technologies (primarily focusing on Aim 1) and their delivery modalities (notably subaim 1.2) to edit specific bacterial genomes of interest to enhance their functionalities, and programmably ablate specific undesirable members of bacterial communities for plant health. We are focusing on engineering bacteriophages (bacterial viruses, for subaim 1.2) to carry programmable CRISPR-Cas systems (subaim 1.1) to target (ablate) or alter (edit) genomes of interest. This will enable us to carry out microbial perturbations that will impact community composition and function and ultimately plant growth and health, to enable the next phase of the project by deploying them in situ (subaims 1.3 and 1.4).

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1981

Development of guayule (Parthenium argentatum) research in cell culture

Utilizing the lateral buds of known high rubber producing plants as explants in culture medium specifically designed to engender shoot development and to prevent callus formation, unlimited numbers of replicate plants can be produced. Each has the same genotype as the parent. This procedure has long been used to rid plants of virus, the latter generally does not occur in the embryonic tissues of the bud; it also, by virtue of its axenic nature, eliminates all microorganisms characteristic of the parent plant. Auxins were found essential to callus formation, but since the latter is known to bring about chromosomal aberrations, it was avoided. The cytokinin benzylaminopurine strongly stimulated shoot growth, and the number of regenerated buds on the inoculum was proportional to its concentration. These buds produced shoots several centimeters in length which were caused to root on medium containing indolebutyric acid. Transferred to the septic condition of soil, the plantlets were gradually brought into full sunlight where they showed a brief vegetative growth with production of mature leaves, and flowered.

Ball, E. A.↗

NASA NTRS2012

Investigating the Potential Range Expansion of the Vector Mosquito Aedes Aegypti in Mexico with NASA Earth Science Remote Sensing Results

In tropical and sub ]tropical regions, the mosquito Aedes aegypti is the major vector for the virus causing dengue, a serious public health issue in these areas. Through ongoing NSF- and NASA-funded studies, field surveys of Aedes aegypti and an integrated modeling approach are being used to improve our understanding of the potential range of the mosquito to expand toward heavily populated high elevation areas such as Mexico City under various climate change and socio ]economic scenarios. This work serves three primary objectives: (1) Employ NASA remotely-sensed data to supplement the environmental monitoring and modeling component of the project. These data-- for example, surface temperature, precipitation, vegetation indices, soil moisture and elevation-- are critical for understanding the habitat necessary for mosquito survival and abundance; (2) Implement training sessions to instruct scientists and students from Mexico and the U.S. on how to use remote sensing and implement the NASA SERVIR Regional Visualization and Monitoring System; (3) Employ the SERVIR framework to optimize the dissemination of key project results in order to increase their societal relevance and benefits in developing climate adaptation strategies. Field surveys of larval, pupal and adult Aedes aegypti, as well as detailed physical and social household characteristics, were conducted in the summers of 2011and 2012 at geographic scales from the household to the community along a transect from sea level to 2400 m ASL. These data are being used in models to estimate Aedes aegypti habitat suitability. In 2011, Aedes aegypti were identified at an elevation of over 2150 m in Puebla, the highest elevation at which this species has been observed.

Crosson, W. L.↗

NASA NTRS1989

Interior Landscape Plants for Indoor Air Pollution Abatement

In this study, the leaves, roots, soil, and associated microorganisms of plants have been evaluated as a possible means of reducing indoor air pollutants. Additionally, a novel approach of using plant systems for removing high concentrations of indoor air pollutants such as cigarette smoke, organic solvents, and possibly radon has been designed from this work. This air filter design combines plants with an activated carbon filter. The rationale for this design, which evolved from wastewater treatment studies, is based on moving large volumes of contaminated air through an activated carbon bed where smoke, organic chemicals, pathogenic microorganisms (if present), and possibly radon are absorbed by the carbon filter. Plant roots and their associated microorganisms then destroy the pathogenic viruses, bacteria, and the organic chemicals, eventually converting all of these air pollutants into new plant tissue. It is believed that the decayed radon products would be taken up the plant roots and retained in the plant tissue.

Wolverton, B. C.↗