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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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Machine learning approaches for integrating multi-omics data to expand microbiome annotation (Final Technical Report)

We fulfilled all original three aims of the proposal. Following the earlier release (during the first phase of the project at Montana) of software that identifies and fills gaps in the annotation of metabolic proteins within bacterial genomes, we have nearly completed a second gap-filling tool that improves accuracy and explainability. We completed software for alignment-based annotation of protein coding DNA, allowing for coding frameshifts caused by sequencing error. Finally, we completed a neural embedding model for identifying similarities between protein sequences based on amino-wise latent vectors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Summary Data for paper titled: Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry

Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. Carbon cycling processes in the surface soil were dominated by plant-microbe interactions that drive organic carbon cycling, whereas inorganic carbon chemistry dominated in deeper soil layers. Both irrigation and plant cover impacted organic and inorganic carbon pools in the soil profiles. This study reveals the complex interactions between water, plants, minerals, and microorganisms that govern organic and inorganic pools of soil carbon at different depths.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Data for Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry: Summary Data

Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. Carbon cycling processes in the surface soil were dominated by plant-microbe interactions that drive organic carbon cycling, whereas inorganic carbon chemistry dominated in deeper soil layers. Both irrigation and plant cover impacted organic and inorganic carbon pools in the soil profiles. This study reveals the complex interactions between water, plants, minerals, and microorganisms that govern organic and inorganic pools of soil carbon at different depths.

Naasko, Katherine I↗
DOE OSTI2023

Data for Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry: Sequence Data

Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. Carbon cycling processes in the surface soil were dominated by plant-microbe interactions that drive organic carbon cycling, whereas inorganic carbon chemistry dominated in deeper soil layers. Both irrigation and plant cover impacted organic and inorganic carbon pools in the soil profiles. This study reveals the complex interactions between water, plants, minerals, and microorganisms that govern organic and inorganic pools of soil carbon at different depths.

Naasko, Katherine I↗
DOE OSTI2025

Limited effects of tannin supplementation on the dairy cattle fecal microbiome with modulation of metabolites

Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.

Klein, Matthew L↗
DOE OSTI2022

The quality of organic amendments affects soil microbiome and nitrogen-cycling bacteria in an organic farming system

Organic amendments are applied in organic farming systems to provide nutrients for crop uptake and to improve soil health. Compost is often favored over fresh manure for food safety reasons, while fresh manure can be a valuable source of readily available nitrogen (N). However, the potential for fresh versus composted manure to differentially affect soil microbial and N-cycling functional communities over multiple seasons remains unknown. We compared the effect of composted vs. fresh cattle manure on soil microbial communities using taxonomic and functional approaches. Soils were collected from field plots with three organic N treatments: control (no amendment), composted manure (compost, 224 kg/ha total N), and fresh manure (manure, 224 kg/ha total N) in an organic production system. Illumina amplicon sequencing was used to comprehensively assess the bacterial community (16S rRNA genes), fungal community (ITS), ureolytic community ( ureC ), chitinolytic community ( chiA ), bacterial ammonia oxidizers (AOB amoA ), and nitrite oxidizers ( Nitrospira nxrB ). The results showed that both compost and manure treatment significantly changed the soil microbial communities. Manure had a stronger effect than compost on soil bacterial and fungal community composition, as well as on the ureolytic and chitinolytic communities, while compost treated soils had higher microbial richness than manure treated soils. Both taxonomic and functional approaches showed that the microbial community was more responsive to fresh manure than to compost. Manure treated soil also had more complex microbial interactions than compost treated soil. The abundance and community composition of N-cycling functional groups often played more limited roles than soil chemical properties (soil organic carbon, extractable organic carbon, and pH) in driving N-cycling processes. Results from our study may guide strategies for the management of organic amendments in organic farming systems and provide insights into the linkages between soil microbial communities and soil function.

Ouyang, Yang↗
DOE OSTI2021

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome

Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue exclusively results from the grass–fungus symbiosis, or this symbiosis additionally results in the recruitment of soil microbes in the rhizosphere that in turn promote plant growth, remain a question. We investigated the soil bacterial and fungal community composition in iron-rich soil in the southeastern USA, and possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Our data revealed that plant-available phosphorus (P) was significantly (p < 0.05) influenced by endophyte infection in tall fescue. While the prominent soil bacterial phyla were similar, a clear fungal community shift was observed between endophyte-infected (E+) and endophyte-free (E−) tall fescue soil at the phylum level. Moreover, compared to E− soil, E+ soil showed a greater fungal diversity at the genus level. Our results, thus, indicate a possible three-way interaction between tall fescue, fungal endophyte, and soil fungal communities resulting in improved tall fescue performance.

Mahmud, Kishan↗