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At least 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Spatial Microbial Respiration Variations in the Hyporheic Zones Within the Columbia River Basin

Abstract While the hyporheic zone (HZ) accounts for a significant portion of whole stream CO 2 concentrations, HZ respiration modeling studies are lacking in quantifying their contributions to the total CO 2 at large watershed/basin scales. Quantifying the contribution of anaerobic respiration is also underappreciated. This study used a carbon‐nitrogen‐coupled river corridor model to quantify HZ aerobic and anaerobic respiration and determined the key factors controlling their spatial variability within the Columbia River Basin (CRB). The modeled respiration patterns showed high spatial variability. Among the nine sub‐basins composing the CRB, the Lower Columbia and the Willamette, which receive higher precipitation, had higher respiration. Medium‐sized rivers (fourth to sixth orders) produced the highest aerobic and anaerobic respiration among reaches of different sizes. At the basin scale, aerobic respiration is dominant, representing approximately 98.7% of the total respiration across the CRB. While most of the reaches were dominant with aerobic respiration, reaches in agricultural land showed a relatively higher anaerobic respiration (18%) ratio. A variable importance analysis showed that hyporheic exchange flux controlled most of the spatial variability of HZ respiration, dominating over other physical variables such as residence time, stream dissolved organic carbon (DOC), nitrate, and dissolved oxygen (DO). The influence of substrate concentration (DOC and DO) is larger in modeling anaerobic respiration than aerobic respiration. Future efforts will focus on improving the estimation of the HZ exchange flux and the implementation of spatially explicit parameterizations for the reactions of interest to reduce model uncertainty.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling

Rice paddies significantly contribute to atmospheric methane (CH 4 ). Here, we show that two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) reduce cumulative CH 4 emissions by 38% (PSY1) and 58% (PSY2) over 70 days of growth compared with controls. Genome-resolved metatranscriptomic data from PSY rhizosphere soils reveal lower ratios of gene activities for (mostly hydrogenotrophic) CH 4 production versus consumption, decreased activity of H 2 -producing genes, and increased activity of bacterial H 2 oxidation pathways. Metabolic modeling using metagenomic and metabolomic data predicts elevated H 2 oxidation and suppressed H 2 production in the PSY rhizosphere. Assembled genomes of rhizosphere H 2 -oxidizing bacteria are enriched in genes utilizing gluconeogenic acids compared with H 2 -producing counterparts, and their activities are likely stimulated by elevated levels of gluconeogenic acids, primarily amino acids, in PSY root exudates. Overall, our study indicates that decreased CH 4 emissions are due to a lower amount of H 2 available for hydrogenotrophic methanogenesis and provides a powerful strategy to mitigate CH 4 emissions from increasingly widespread rice cultivation.

Biological and medical sciences↗
DOE OSTI2026

Isolation of genome-predicted Caldatribacterium ( Atribacterota ) reveals pervasive microbial cultivation problem due to folate precipitation

Most bacterial phyla have few or no pure cultures, including Atribacterota , comprised of ubiquitous anaerobes. Here, we report genome-guided enrichment and isolation of two Atribacterota species representing a new family, Caldatribacterium saccharofermentans from a hot spring, and Caldatribacterium inferamans from a deep aquifer. Both were co-enriched with sulfate-reducing bacteria and initially resisted isolation, which we link to inadvertent removal of precipitated folic acid by filter-sterilization of unbuffered Wolin’s vitamin solution. We then predict folate auxotrophy across the Atribacterota and ~29% of all bacteria, with extensive auxotrophy in 27% of phyla. Since ≥604 of 791 ( ≥ 76%) media with folic acid additions in the MediaDive database use unbuffered vitamin solutions in which folic acid is likely removed during filter-sterilization, we propose that folate auxotrophy limits culturability in defined media en masse. We also uncover unusual features of Caldatribacterium , including three lipid membrane-like layers (LMLs), with the inner LML surrounding the nucleoid, and a high percentage of secreted proteins, supporting a unique cell biology of Atribacterota .

Biological and medical sciences↗
DOE OSTI2021

Microbial production of advanced biofuels

Concerns over climate change have necessitated a rethinking of our transportation infrastructure. One possible alternative to carbon-polluting fossil fuels is biofuels produced by engineered microorganisms that use a renewable carbon source. Two biofuels, ethanol and biodiesel, have made inroads in displacing petroleum-based fuels, but their uptake has been limited by the amounts that can be used in conventional engines and by their cost. Further, advanced biofuels that mimic petroleum-based fuels are not limited by the amounts that can be used in existing transportation infrastructure but have had limited uptake due to costs. In this Review, we discuss engineering metabolic pathways to produce advanced biofuels, challenges with substrate and product toxicity with regard to host microorganisms and methods to engineer tolerance, and the use of functional genomics and machine learning approaches to produce advanced biofuels and prospects for reducing their costs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A toolkit for microbial community editing

This month’s Genome Watch highlights recently reported methods that enable genome editing of microorganisms within phylogenetically diverse communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Electric field stimulates production of highly conductive microbial OmcZ nanowires

Multifunctional living materials are attractive due to their powerful ability to self-repair and replicate. However, most natural materials lack electronic functionality. Here we show that an electric field, applied to electricity-producing Geobacter sulfurreducens biofilms, stimulates production of cytochrome OmcZ nanowires with 1,000-fold higher conductivity (30 S cm -1 ) and threefold higher stiffness (1.5 GPa) than the cytochrome OmcS nanowires that are important in natural environments. Using chemical imaging-based multimodal nanospectroscopy, we correlate protein structure with function and observe pH-induced conformational switching to β-sheets in individual nanowires, which increases their stiffness and conductivity by 100-fold due to enhanced π-stacking of heme groups; this was further confirmed by computational modeling and bulk spectroscopic studies. These nanowires can transduce mechanical and chemical stimuli into electrical signals to perform sensing, synthesis and energy production. Overall, these findings of biologically produced, highly conductive protein nanowires may help to guide the development of seamless, bidirectional interfaces between biological and electronic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Mapping microhabitats of lignocellulose decomposition by a microbial consortium

The leaf-cutter ant fungal garden ecosystem is a naturally evolved model system for efficient plant biomass degradation. Degradation processes mediated by the symbiotic fungus Leucoagaricus gongylophorus are difficult to characterize due to dynamic metabolisms and spatial complexity of the system. Herein, we performed microscale imaging across 12-µm-thick adjacent sections of Atta cephalotes fungal gardens and applied a metabolome-informed proteome imaging approach to map lignin degradation. This approach combines two spatial multiomics mass spectrometry modalities that enabled us to visualize colocalized metabolites and proteins across and through the fungal garden. Spatially profiled metabolites revealed an accumulation of lignin-related products, outlining morphologically unique lignin microhabitats. Metaproteomic analyses of these microhabitats revealed carbohydrate-degrading enzymes, indicating a prominent fungal role in lignocellulose decomposition. Integration of metabolome-informed proteome imaging data provides a comprehensive view of underlying biological pathways to inform our understanding of metabolic fungal pathways in plant matter degradation within the micrometer-scale environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Author Correction: Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days

In the version of this article initially published, two errors in authorship were made. First, Tatiana Rynearson of the School of Oceanography, University of Rhode Island was mistakenly omitted from the final author list. Second, Kurt LaButti of the Joint Genome Institute was mistakenly omitted from the final author list and replaces Alicia Clum due to a staffing change at the Joint Genome Institute. These authorship omissions were not identified until after the work had been published. We are updating the authorship to appropriately recognize the contributions of these authors. The error has been corrected in the PDF and HTML versions of the article.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life

There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.

59 BASIC BIOLOGICAL SCIENCES↗