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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 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion ( >55%) of the community is composed of poorly characterized low abundance (individually <1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. In conclusion, these results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity

Cactaceae represents one of the most species-rich families of succulent plants native to arid and semi-arid ecosystems, yet the associations Cacti establish with microorganisms and the rules governing microbial community assembly remain poorly understood. We analyzed the composition, diversity, and factors influencing above- and below-ground bacterial, archaeal, and fungal communities associated with two native and sympatric Cacti species: Myrtillocactus geometrizans and Opuntia robusta. Phylogenetic profiling showed that the composition and assembly of microbial communities associated with Cacti were primarily influenced by the plant compartment; plant species, site, and season played only a minor role. Remarkably, bacterial, and archaeal diversity was higher in the phyllosphere than in the rhizosphere of Cacti, while the opposite was true for fungi. Semi-arid soils exhibited the highest levels of microbial diversity whereas the stem endosphere the lowest. Despite their taxonomic distance, M. geometrizans and O. robusta shared most microbial taxa in all analyzed compartments. Influence of the plant host did only play a larger role in the fungal communities of the stem endosphere. These results suggest that fungi establish specific interactions with their host plant inside the stem, whereas microbial communities in the other plant compartments may play similar functional roles in these two species. Biochemical and molecular characterization of seed-borne bacteria of Cacti supports the idea that these microbial symbionts may be vertically inherited and could promote plant growth and drought tolerance for the fitness of the Cacti holobiont. We envision this knowledge will help improve and sustain agriculture in arid and semi-arid regions of the world.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Soil Microbiome Dynamics During Pyritic Mine Tailing Phytostabilization: Understanding Microbial Bioindicators of Soil Acidification

Challenges to the reclamation of pyritic mine tailings arise from in situ acid generation that severely constrains the growth of natural revegetation. While acid mine drainage (AMD) microbial communities are well-studied under highly acidic conditions, fewer studies document the dynamics of microbial communities that generate acid from pyritic material under less acidic conditions that can allow establishment and support of plant growth. This research characterizes the taxonomic composition dynamics of microbial communities present during a 6-year compost-assisted phytostabilization field study in extremely acidic pyritic mine tailings. A complementary microcosm experiment was performed to identify successional community populations that enable the acidification process across a pH gradient. Taxonomic profiles of the microbial populations in both the field study and microcosms reveal shifts in microbial communities that play pivotal roles in facilitating acidification during the transition between moderately and highly acidic conditions. The potential co-occurrence of organoheterotrophic and lithoautotrophic energy metabolisms during acid generation suggests the importance of both groups in facilitating acidification. Taken together, this research suggests that key microbial populations associated with pH transitions could be used as bioindicators for either sustained future plant growth or for acid generation conditions that inhibit further plant growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2017

Taxonomic and Functional Diversity of a Quercus pyrenaica Willd. Rhizospheric Microbiome in the Mediterranean Mountains

Altitude significantly affects vegetation growth and distribution, including the developmental stages of a forest. We used shotgun Illumina sequencing to analyze microbial community composition and functional potential in melojo-oak ( Quercus pyrenaica Willd.) rhizospheric soil for three different development stages along an altitudinal gradient: (a) a low altitude, non-optimal site for forest maintenance; (b) an intermediate altitude, optimal site for a forest; and (c) a high altitude, expansion site with isolated trees but without a real forest canopy. We observed that, at each altitude, the same microbial taxa appear both in the taxonomic analysis of the whole metagenome and in the functional analysis of the methane, sulfur and nitrogen metabolisms. Although there were no major differences at the functional level, there were significant differences in the abundance of each taxon at the phylogenetic level between the rhizospheres of the forest (low and intermediate altitudes) and the expansion site. Proteobacteria and Actinobacteria were the most differentially abundant phyla in forest soils compared to the expansion site rhizosphere. Moreover, Verrucomicrobia, Bacteroidetes and Nitrospirae phyla were more highly represented in the non-forest rhizosphere. Our study suggests that rhizospheric microbial communities of the same tree species may be affected by development stage and forest canopy cover via changes in soil pH and the C/N ratio.

59 BASIC BIOLOGICAL SCIENCES↗
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↗
DOE OSTI2019

Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome

The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication

Background Premastication, the transfer of pre-chewed food, is a common infant and young child feeding practice among the Tsimane, forager-horticulturalists living in the Bolivian Amazon. Research conducted primarily with Western populations has shown that infants harbor distinct oral microbiota from their mothers. Premastication, which is less common in these populations, may influence the colonization and maturation of infant oral microbiota, including via transmission of oral pathogens. We collected premasticated food and saliva samples from Tsimane mothers and infants (9–24 months of age) to test for evidence of bacterial transmission in premasticated foods and overlap in maternal and infant salivary microbiota. We extracted bacterial DNA from two premasticated food samples and 12 matched salivary samples from maternal-infant pairs. DNA sequencing was performed with MiSeq (Illumina). We evaluated maternal and infant microbial composition in terms of relative abundance of specific taxa, alpha and beta diversity, and dissimilarity distances. Results The bacteria in saliva and premasticated food were mapped to 19 phyla and 400 genera and were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The oral microbial communities of Tsimane mothers and infants who frequently share premasticated food were well-separated in a non-metric multi-dimensional scaling ordination (NMDS) plot. Infant microbiotas clustered together, with weighted Unifrac distances significantly differing between mothers and infants. Infant saliva contained more Firmicutes ( p < 0.01) and fewer Proteobacteria ( p < 0.05) than did maternal saliva. Many genera previously associated with dental and periodontal infections, e.g. Neisseria , Gemella , Rothia , Actinomyces , Fusobacterium , and Leptotrichia , were more abundant in mothers than in infants. Conclusions Salivary microbiota of Tsimane infants and young children up to two years of age do not appear closely related to those of their mothers, despite frequent premastication and preliminary evidence that maternal bacteria is transmitted to premasticated foods. Infant physiology and diet may constrain colonization by maternal bacteria, including several oral pathogens.

Han, Cliff S.↗
NASA NTRS2018

Investigating Microbiome Differences Between Red Romaine Lettuce Grown from Sanitized and Unsanitized Seeds

The International Space Station (ISS) as an integral component for the discovery and development of advanced robotics, materials, communications, medicine, agriculture, and environmental science due to it currently being the world's only microgravity laboratory of its kind. Because the ISS is a contained system with confined quarters, much research has been undertaken to assess and diminish the number of microbiological risks associated with astronauts inhabiting the station for extended periods of time. Notable microbiological risk factors include drinking water, air, and food. As an avenue for both mental/emotional respite and a source of fresh produce for astronauts, a vegetable production system has been employed on the ISS. In order to understand the microbial risks involved with a "pick and eat" vegetable system on the International Space Station (ISS), this study aims to compare microbial differences between sanitized and unsanitized seeds by tracking and identifying seedborne microbes throughout the development of red romaine lettuce (Lactuca sativa)-a plant species that has already been grown on the ISS.

Polanco, Jonilee A.↗
NASA NTRSDate not supplied

Plant Microbiome 101

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Anirudha R. Dixit↗