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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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28 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

Hagen, Live↗
DOE OSTI2022

Anaerobic Degradation of Alkanes by Marine Archaea

Alkanes are saturated apolar hydrocarbons that range from their simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea.

Microbiology↗
DOE OSTI2025

Metagenome‐Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain

Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. In conclusion, the SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

KBase Silver Case Study: Determining Media Formulation Requirements for Isolation of Microbiome Constituents

KBase has powerful tools for extracting microbial genomes from metagenomes and performing phylogenomic analysis and metabolic modeling. These tools can be used to predict key media ingredients for isolating uncultured members of microbiomes. Essential to this process are high-quality genomes extracted from metagenomic assemblies, and Kbase has a tool for assessing the quality of genomes too. Below we identify growth factors for a myxobacteria ("slime bacteria") yet to be isolated from the rhizosphere of Miscanthus xgiganteus (hybrid of "Silvergrass"), cultivated at the Kellogg Biological Station in Michigan. Data was transferred with Globus from JGI-IMG. This narrative and the "KBase Gold Case Study: Can you find Delftia?" make up the Silver and Gold Narrative Set for teaching metagenomics concepts to students in the BIT 477/577 course at North Carolina State University. This tutorial will guide the user through the process of extracting and annotating high-quality genomes from a metagenomic data, performing phylogenomic analysis, building a metabolic model, and using these to predict nutrient requirments for growth and isolation of corresponding microbes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Respiration-driven methanotrophic growth of diverse marine methanogens

Anaerobic marine environments are the third largest producer of the greenhouse gas methane. The release to the atmosphere is prevented by anaerobic ‘methanotrophic archaea (ANME) dependent on a symbiotic association with sulfate-reducing bacteria or direct reduction of metal oxides. Metagenomic analyses of ANME are consistent with a reverse methanogenesis pathway, although no wild-type isolates have been available for validation and biochemical investigation. Herein is reported the characterization of methanotrophic growth for the diverse marine methanogens Methanosarcina acetivorans C2A and Methanococcoides orientis sp. nov. Growth was dependent on reduction of either ferrihydrite or humic acids revealing a respiratory mode of energy conservation. Acetate and/or formate were end products. In conclusion, reversal of the well-characterized methanogenic pathways is remarkably like the consensus pathways for uncultured ANME based on extensive metagenomic analyses.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Organization of P, S, and Fe Inclusions in a Freshwater Magnetococcus

Magnetotactic bacteria are a heterogeneous group of motile, mainly aquatic procaryotes that align and swim along geomagnetic field lines. They are of interest to astrobiologists because of the magnetite crystals found in the Mars meteorite ALH84001 which share many characteristics with the magnetite produced intracellularly by magnetotactic bacteria. These bacteria are diverse morphologically, physiologically and phylogenetically, sharing a few key characteristics: 1) the presence of intracellular membrane-bound magnetic crystals (magnetosomes), usually but not always arranged in chains; 2) motility by means of flagella; and 3) microaerophillic or anaerobic physiology. The bilophotrichous (having two flagella bundles) magnetotactic cocci (MC) are ubiquitous in aquatic habitats but have proven extremely difficult to cultivate. Because only several marine strains have been isolated and grown in axenic culture, little is known about the physiology and the biogeochemical roles of the MC. We studied the composition and distribution of intracellular structures in an uncultured MC, designated ARB-1. To do this, a combination of light microscopy, environmental scanning electron microscopy (ESEM), transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDS) were used. Cells of ARB-1 were separated from sediments collected from Baldwin Lake (Los Angeles Arboretum, Arcadia, CA). They are large spherical to oblate spheroidal Gram-negative cells, ranging from 1 to 4 micrometers along the maximum dimension, which is perpendicular to the direction of swimming. Cells have two large phosphorus-containing inclusions that comprise a large percentage of the cell volume. Many smaller sulfur inclusions are located at the convex end of the cell. Most of the cellular Fe is present in the magnetosomes. These may be arranged as a clump at the concave end of the cell, near the two flagella bundles, or as chains, or as both a clump and chains. The magnetosomes were identified as magnetite (Fe3O4) by selected area electron diffraction (SAED) and high resolution TEM. We saw a trend between cell size and organization of the magnetosomes. Smaller, more spherical cells were more likely to have chains than were larger, more oblate cells. This may indicate different populations of cells, or it may be attributed to variations in cell growth cycle. The size distribution (length) of magnetosomes in chains was similar to that of magnetosomes in clusters, except that there was a larger size range for clustered magnetosomes. Magnetosomes from ARB-1 cells average 82 nm in length. If plotted on a graph of length as a function of aspect ratio, they fall within the single domain region of the plot. If compared with the size distributions of magnetite from ALH84001 and magnetosomes from the cultured magnetotactic vibrio MV-1, the magnetites produced by ARB-1 cells are, on average, larger and have a wider range of aspect ratio. ARB-1 cells have a specific organization of the P, S, and Fe inclusions. The P inclusions always occupy the majority of the cell volume and separate the S inclusions from the disorganized clumps of magnetosomes and the flagella bundles. The P inclusions may contain polyphosphate, which could play several roles in motility, adaptation to stress, growth and division, buoyancy, and energy. The S inclusions might be a way to store S, a potential energy source, when the cells move from sulfide to oxygen zones. The consistency of P, S, and Fe organization in ARB-1 cells suggests that these inclusions have some specific and interactive functions.

Cox, Lea↗
NASA NTRS2002

Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology

A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis.

Non-NASA Center↗
NASA NTRS2003

Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin

The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (dsrAB) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The dsrAB sequences revealed that there was a major clade closely related to the acetate-oxidizing delta-proteobacterial genus Desulfobacter and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other dsr clones were affiliated with gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the delta-proteobacterial species Desulforhabdus amnigena and Thermodesulforhabdus norvegica. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with Desulfobacterium niacini, a member of the acetate-oxidizing, nutritionally versatile genus Desulfobacterium, and one clone related to Desulfobacula toluolica and Desulfotignum balticum. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and dsrAB clone libraries resulted in identification of members of the Desulfobacteriales in the Guaymas sediments. In addition, the dsrAB sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing.

Non-programmatic↗
DOE OSTI2022

Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence

We report interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H 2 O 2 . Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Previously uncharacterized rectangular bacterial structures in the dolphin mouth

Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining revealed multiple paired bands within RBSs, suggesting the presence of cells dividing along the longitudinal axis. Cryogenic transmission electron microscopy and tomography showed parallel membrane-bound segments that are likely cells, encapsulated by an S-layer-like periodic surface covering. RBSs displayed unusual pilus-like appendages with bundles of threads splayed at the tips. We present multiple lines of evidence, including genomic DNA sequencing of micromanipulated RBSs, 16S rRNA gene sequencing, and fluorescence in situ hybridization, suggesting that RBSs are bacterial and distinct from the genera Simonsiella and Conchiformibius (family Neisseriaceae), with which they share similar morphology and division patterning. Our findings highlight the diversity of novel microbial forms and lifestyles that await characterization using tools complementary to genomics such as microscopy.

59 BASIC BIOLOGICAL SCIENCES↗