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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

BRCore: an R package implementing flexible selection of core taxa using contribution to Bray-Curtis dissimilarity and neutral model fitting

Identifying core taxa in microbial ecology highlights groups likely to participate in a broad range of potential ecological interactions. Here, we present BRCore, an R package to identify core taxa using abundance-occupancy distributions and beta-diversity contributions across ecological niches, and predict stochastic and deterministic taxa.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multidimensional scaling informed by F -statistic: Visualizing grouped microbiome data with inference

Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. Here, in this study, we introduce a new MDS-based ordination method, “F-informed MDS,” which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community’s response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.

Biological and medical sciences↗
DOE OSTI2025

Identifying microbial functional guilds performing cryptic organotrophic and lithotrophic redox cycles in anaerobic granular biofilms

Granular biofilms used in anaerobic digester systems contain diverse microbial populations that interact to hydrolyze organic matter and produce methane within controlled environments. Prior research investigated the feasibility of utilizing granular biofilms obtained from an anaerobic digester to remove nitrate without the addition of exogenous electron donors. These granules possessed a unique structure of alternating light and dark iron sulfide and pyrite rich layers that potentially served as both an electron source and sink, linking carbon, nitrogen, sulfur, and iron cycles. To characterize the functional roles of diverse microbial populations enriched within these layered biofilms, we analyzed metagenomes obtained from three different granules. Comparisons between the functional gene content of forty metagenome assembled genomes (MAGs) identified phylogenetically cohesive functional guilds. Each of these functional MAG clusters was assigned to specific steps in anaerobic digestion (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) and anaerobic respiration (denitrification and sulfate reduction). Comparisons with metagenomes derived from a variety of natural and engineered ecosystems confirmed that the enriched denitrifying bacteria were similar to populations typically found in wetlands and biological nitrogen removal systems. Analysis of read alignments to individual genes within the forty MAGs identified conserved genomic features that were representative of the functions that distinguished functional guilds. Overall, this research illustrates the utility of functional based classification of microorganisms for characterizing ecosystem functions and highlights the potential application of engineered ecosystems to serve as experimental models for complex natural ecosystems.

Ecosystem engineering↗
DOE OSTI2025

Montane Conifer, Aspen, Meadow, and Sagebrush Metagenome Resolved Genomes and Traits in East River Watershed, Colorado, USA

Climate change is driving vegetation shifts in mountain watersheds, with unknown impacts on biogeochemical cycles. We hypothesize that these shifts will reshape soil microbiomes and associated biogeochemical processes. As a part of Lawrence Berkeley National Laboratory (LBNL) Watershed Science Focus Area (SFA), we assessed microbiome and microbial functional trait differences between soils under conifer, aspen, forby meadows, and sagebrush across the East River Watershed, CO, controlling for elevation and aspect.Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from soils 0-20cm in depth across three locations in the watershed—Headwaters, Upper Reaches, and Lower Reaches from August 3-11th 2016. Each location was further subdivided into two blocks, with one block on a west facing aspect, and two on the east aspect of the valley. Within blocks, two samples per vegetation type were taken (one at each depth). This resulted in 66 samples, which were sequenced at JGI and can be found under the Joint Genome Institute (JGI) Genomes Online Database (GOLD) sequencing project Gs0118068. Metagenomes were assembled through an inhouse pipeline (see methods), binned using four autobinners (concoct, maxbin2, metabat2, and vamb) and consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>75%) and contamination (<25%), and dereplicated at 95% ANI using drep. The dataset includes a zip file of 687 genomes (Vegtype_MAGS.zip), the accession numbers for the underlying metagenomes, a csv file with MAG quality metrics and taxonomy from Genome Taxonomy Database (GTDB) and National Center for Biotechnology Information (NCBI) taxonomic representative genome proteins (EastRiver_Vegtype_drep_genome_info.csv), and a file containing MAG quality metrics and taxonomy (gtdb_drep_bin_taxonomy.csv). The dataset additionally includes a sample metadata file (EastRiver_Vegtype_sample_metadata.csv), a metadata file used to register associated samples with IGSNs (International Generic Sample Numbers) (samples.csv), a Google KML file for the sampled locations (sample_collection_sites.kml), a location metadata file (locations.csv), a file-level metadata file (flmd.csv), and a data dictionary (dd.csv) file.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.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA): Molecular and Computational Technologies for Environmental Microbiology (Final Scientific/Technical Report)

The ENIGMA science focus area (SFA) is a multi-disciplinary, multi-institutional research effort focused on addressing foundational knowledge gaps in environmental microbial communities by studying groundwater and sediment microbiomes in the shallow subsurface at the contaminated Oak Ridge Reservation (ORR). We seek to discover and characterize the reciprocal interactions between the microbial communities and the geochemical and geophysical parameters of the shallow subsurface within the contamination plume. The primary goal of this subcontract was to develop experimental and computational tools to advance our understanding of microbial adaptation and community assembly in contaminated environments, with specific efforts in high-throughput genomic methods, microbial ecology tools, and studies of heavy metal contamination impacts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

2024 International Conference on Microbiome Engineering (ICME)

The 2024 International Conference on Microbiome Engineering (ICME) took place November 12-14 at Tufts University in Medford, MA. ICME connects experts from academia and industry to share the most recent developments in the field of microbiome engineering. This includes genetically engineered organisms that function within microbiomes, control of microbiomes through environmental/nutrient modifications, and inference of engineering principles from analysis of synthetic and natural microbiomes. The conference is unique and distinct from other microbiome conferences in that it specifically highlights the integration of engineering design principles with microbiome research (others are more focused on basic biological principles). The conference thus integrates synthetic biology, systems biology, microbial ecology, and bioinformatics across a range of application spaces from the environment to manufacturing, food, and human health. This project utilized support from the Department of Energy’s (DOE) Office of Biological and Environmental Research (BER) to help trainees and early career faculty attend ICME.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Potential applications of microbial genomics in nuclear non-proliferation

As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as “characteristic communities of microorganisms” found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2024

Transporter annotations are holding up progress in metabolic modeling

Mechanistic, constraint-based models of microbial isolates or communities are a staple in the metabolic analysis toolbox, but predictions about microbe-microbe and microbe-environment interactions are only as good as the accuracy of transporter annotations. A number of hurdles stand in the way of comprehensive functional assignments for membrane transporters. These include general or non-specific substrate assignments, ambiguity in the localization, directionality and reversibility of a transporter, and the many-to-many mapping of substrates, transporters and genes. In this perspective, we summarize progress in both experimental and computational approaches used to determine the function of transporters and consider paths forward that integrate both. Investment in accurate, high-throughput functional characterization is needed to train the next-generation of predictive tools toward genome-scale metabolic network reconstructions that better predict phenotypes and interactions. More reliable predictions in this domain will benefit fields ranging from personalized medicine to metabolic engineering to microbial ecology.

Casey, John↗
NASA NTRS1985

Chemolithotrophy and physiology of bacterial nutrient limitation

An overview of the physiology of chemolithotrophic bacteria, particularly the thiobacilli, was presented. In these bacteria unique physiological traits are expressed during nutrient limited growth. Different physiological types of chemolithotrophs, pathways of sulfur oxidation, and electron transport in the thiobacilli, problems encountered by chemolithotrophs in the generation of reducing power, and some explanations of the phenomenon of obligate chemolithotrophy were considered. Mixotrophy in the thiobacilli has been studied extensively both under nutrient excess and limitation. In nature, bacteria usually grow under nutrient limitation. Yet the bulk of our knowledge of microbial metabolic function is derived from bacteria grown in laboratory batch cultures containing a great abundance of nutrients. Microbial behavior in these two types of environments can be very different, indicating the need for basing an understanding of microbial ecology on studies that rely on cultivation of microorganisms under nutrient limitation. Nutrient limited bacteria differ in several ways from those growing in large quantities of nutrients. They have different surface structures and make a much fuller use of their metabolic potential, especially by the synthesis of unique pathways of catabolic enzymes.

Matin, A.↗
NASA NTRS1994

Exobiology site priorities for Mars Pathfinder

The fact that life developed on the Earth within the first billion years of its history makes it quite plausible that life may have also developed on Mars. If life did develop on Mars, it undoubtedly left behind a fossil record. Such a fossil record is likely to be more accessible than either subsurface environments that may harbor life, or scattered 'oases' that may be present at the surface. Consequently, the post-Viking approach of Mars exobiology has shifted focus to search for evidence of an ancient martian biosphere. This has led to the emergence of a new subdiscipline of paleontology, herein termed 'exopaleontology', which deals with the exploration for fossils on other planets and whose core concepts derive from Earth-based Precambrian paleontology, microbial ecology, and sedimentology. Potential targets on Mars for subaqueous spring deposits, sedimentary cements, and evaporites are ancient terminal lake basins where hydrological systems could have endured for some time under arid conditions. Potential targets for the Mars Pathfinder mission include channeled impact craters and areas of deranged drainage associated with outflows in northwest Arabia and Xanthe Terra, where water may have ponded temporarily to form lakes. The major uncertainty of such targets is their comparatively younger age and the potentially short duration of hydrological activity compared to older paleolake basins found in the southern hemisphere. However, it has been suggested that cycles of catastrophic flooding associated with Tharsis volcanism may have sustained a large body of water, Oceanus Borealis, in the northern plains area until quite late in martian history. Although problematic, the shoreline areas of the proposed northern ocean provide potential targets for a Mars Pathfinder mission aimed at exploring for carbonates or other potentially fossiliferous marine deposits. Carbonates and evaporites possess characteristic spectra signatures in the near-infrared and should be detectable using rover-based spectroscopy and other methods for in situ mineralogical analysis.

Farmer, Jack D.↗
NASA NTRS1997

Searching for Biogeochemical Cycles on Mars

The search for life on Mars clearly benefits from a rigorous, yet broad, definition of life that compels us to consider all possible lines of evidence for a martian biosphere. Recent studies in microbial ecology illustrate that the classic definition of life should be expanded beyond the traditional definition of a living cell. The traditional defining characteristics of life are threefold. First, life is capable of metabolism, that is, it performs chemical reactions that utilize energy and also synthesize its cellular constituents. Second, life is capable of self-replication. Third, life can evolve in order to adapt to environmental changes. An expanded, ecological definition of life also recognizes that life is a community of organisms that must interact with their nonliving environment through processes called biogeochemical cycles. This regenerative processing maintains, in an aqueous conditions, a dependable supply of nutrients and energy for growth. In turn, life can significantly affect those processes that control the exchange of materials between the atmosphere, ocean, and upper crust. Because metabolic processes interact directly with the environment, they can alter their surroundings and thus leave behind evidence of life. For example, organic matter is produced from single-carbon-atom precursors for the biosynthesis of cellular constituents. This leads to a reservoir of reduced carbon in sediments that, in turn, can affect the oxidation state of the atmosphere. The harvesting of chemical energy for metabolism often employs oxidation-reduction reactions that can alter the chemistry and oxidation state of the redox-sensitive elements carbon, sulfur, nitrogen, iron, and manganese. Have there ever been biogeochemical cycles on Mars? Certain key planetary processes can offer clues. Active volcanism provides reduced chemical species that biota can use for organic synthesis. Volcanic carbon dioxide and methane can serve as greenhouse gases. Thus the persistence of volcanism on Mars may well have influenced the persistence of a martian biosphere. The geologic processing of the crust can affect the availability of nutrients and also control the deposition of minerals that could have served as a medium for the preservation of fossil information. Finally, the activity of liquid water is crucial to life. Was there ever an Earth-like hydrologic cycle with rainfall? Has aqueous activity instead been restricted principally to hydrothermal activity below the surface? To what extent did the inorganic chemistry driven by sunlight and hydrothermal activity influence organic chemistry (prebiotic chemical evolution)? This paper addresses these and other key questions.

DesMarais, David J.↗
NASA NTRS1997

A low molecular weight artificial RNA of unique size with multiple probe target regions

Artificial RNAs (aRNAs) containing novel sequence segments embedded in a deletion mutant of Vibrio proteolyticus 5S rRNA have previously been shown to be expressed from a plasmid borne growth rate regulated promoter in E. coli. These aRNAs accumulate to high levels and their detection is a promising tool for studies in molecular microbial ecology and in environmental monitoring. Herein a new construct is described which illustrates the versatility of detection that is possible with aRNAs. This 3xPen aRNA construct carries a 72 nucleotide insert with three copies of a unique 17 base probe target sequence. This aRNA is 160 nucleotides in length and again accumulates to high levels in the E. coli cytoplasm without incorporating into ribosomes. The 3xPen aRNA illustrates two improvements in detection. First, by appropriate selection of insert size, we obtained an aRNA which provides a unique and hence, easily quantifiable peak, on a high resolution gel profile of low molecular weight RNAs. Second, the existence of multiple probe targets results in a nearly commensurate increase in signal when detection is by hybridization. These aRNAs are naturally amplified and carry sequence segments that are not found in known rRNA sequences. It thus may be possible to detect them directly. An experimental step involving RT-PCR or PCR amplification of the gene could therefore be avoided.

Non-NASA Center↗
NASA NTRS1999

A new version of the RDP (Ribosomal Database Project)

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.

Non-NASA Center↗
NASA NTRS1994

Biomass Burning and the Production of Greenhouse Gases

Biomass burning is a source of greenhouse gases, carbon dioxide, methane, and nitrous oxide. In addition, biomass burning is a source of chemically active gases, including carbon monoxide, nonmethane hydrocarbons, and nitric oxide. These gases, along with methane, lead to the chemical production of tropospheric ozone (another greenhouse gas) as well as control the concentration of the hydroxyl radical, which regulates the lifetime of almost every atmospheric gas. Following biomass burning, biogenic emissions of nitrous oxide, nitric oxide, and methane are significantly enhanced. It is hypothesized that enhanced postburn biogenic emissions of these gases are related to fire-induced changes in soil chemistry and/or microbial ecology. Biomass burning, once believed to be a tropical phenomenon, has been demonstrated by satellite imagery to also be a regular feature of the world's boreal forests. One example of biomass burning is the extensive 1987 fire that destroyed more than 12 million acres of boreal forest in the People's Republic of China and across its border in the Soviet Union. Recent estimates indicate that almost all biomass burning is human-initiated and that it is increasing with time. With the formation of greenhouse and chemically active gases as direct combustion products and a longer-term enhancement of biogenic emissions of gases, biomass burning may be a significant driver for global change.

Levine, Joel S.↗
NASA NTRS2005

Autonomy Software Architecture for LORAX (Life On ice Robotic Antarctic eXplorer)

LORAX is a robotic astrobiological study of the ice field surrounding the Carapace Nunatak near the Allan Hills in Antarctica. The study culminates in a l00km traverse, sampling the ice at various depths (from surface to 10cm) at over 100 sites to survey microbial ecology and to record environmental parameters. The autonomy requirements from LORAX are shared by many robotic exploration tasks. Consequently, the LORAX autonomy architecture is a general architecture for on-board planning and execution in environments where science return is to be maximized against resource limitations and other constraints.

Jonsson, Ari↗
NASA NTRS2019

New Technologies for Enabling Food Production Beyond LEO

NASA has identified the need for robust and sustainable ‘Pick-and-Eat’ systems for supplementing crew diets with fresh leafy green crops in near-term LEO (Low Earth Orbit), cislunar, and lunar missions. Spaceflight plant growth systems have been primarily designed for conducting space biology studies, but these systems are not optimal for sustained food production. Improved water and nutrient delivery subsystems that do not use bulky and non-reusable media are needed for decreasing the mass of the food production system. Autonomous technologies for monitoring plant health and food safety are needed for ensuring that the food produced is suitable supplementing crew diets with fresh, nutritious salad crops. Improved plant imaging techniques used for high-throughput phenotyping can be leveraged for monitoring plant health. Near-real-time measurements of the microbial ecology of food production systems are needed for assessing food safety. Furthermore, newly identified plant species and cultivars with improved growth habits and contents of antioxidants, vitamins, and minerals when grown in spaceflight environmental conditions are needed. These improvements in food production technologies will enable the design of sustainable life support systems for manned exploration missions beyond Low Earth Orbit.

Monje Mejia, Oscar A.↗