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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Microbial assimilation of lignin-derived aromatic compounds and conversion to value-added products

Lignin is an abundant and sustainable source of aromatic compounds that can be converted to value-added products. However, lignin is underutilized, since depolymerization produces a complex mixture of aromatic compounds that is difficult to convert to a single product. Microbial conversion of mixed aromatic substrates provides a potential solution to this conversion challenge. Recent advances have expanded the range of lignin-derived aromatic substrates that can be assimilated and demonstrated efficient conversion via central metabolism to new potential products. Here, the development of additional non-model microbial hosts and genetic tools for these hosts have accelerated engineering efforts. However, yields with real depolymerized lignin are still low, and additional work will be required to achieve viable conversion processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Plant-microbial interplay for organic nitrogen mediated by functional specificity of root compartments

The organic form of nitrogen (N) is a critical intermediate in mutualistic and competitive root-microbial interactions, mediated by extracellular enzymes. Visualization of the hotspots of organic N and proteolytic activity might be valuable for revealing root functional specificity in N acquisition and transformation at the level of individual roots and compartments. For the first time, we used time-lapse amino-mapping and zymography to co-localize and map the spatial distribution of amino-N and leucine aminopeptidase (LAP) activity in the soil and different root parts of maize (Zea mays L.). Amino-N distribution was mainly associated with seminal roots and root tips, where it overlapped with LAP activity hotspots. In the lateral roots and bulk soil, however, LAP activity was decoupled from amino-N. Distinct functional traits revealed themselves as the highest amino-N content and LAP activity in seminal root tips and as the largest relative extent of the rhizosphere in lateral root tips. Co-localized amino-N and LAP activities highlighted different nutrient acquisition strategies mediated by root-microbe interactions, depending on the root compartment. Seminal roots and their tips appeared to adopt mutualistic strategies, potentially attracting root-associated microorganisms through releasing oligo- and polypeptides. In contrast, lateral roots, with amino-N detected only at their tips, demonstrated stronger N competition, relying on the enzyme activity of the rhizosphere microbial community for N acquisition. These insights emphasized the role of root functional specialization in shaping plant-microbe interactions, offering pathways to enhance nutrient use efficiency.

Maize (Zea mays L.)↗
DOE OSTI2025

Molecular Imaging of Microbially Induced Corrosion of Synthetic Archeological Glasses by a Rhizosphere Bacterium

Microbially induced corrosion (MIC) focuses on the degradation of solid materials, such as glass or metal. Soil microbes are often associated with the corrosion of foreign objects in the rhizosphere. Paenibacillus polymyxa SCE2, a facultative anaerobic bacterium in soil, is of the same genus as bacteria found near nuclear waste disposal sites. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used for imaging surface changes induced by P. polymyxa SCE2 cultured on two synthetic glass coupons to represent natural analogs of materials that were studied in relation to the vitrification of nuclear waste. Multimodal imaging was used to verify bacterial coverage across the glass surface after long-term growth. ToF-SIMS spectral analysis showed detection of glass component ions, such as silicon oxide (m/z – 59.96 SiO 2 – ) and aluminum oxide (m/z – 101.95 Al 2 O 3 – ), and biofilm’s extracellular polymeric substance (EPS) components, such as pentadecanoic acid (m/z – 241.22 C 15 H 29 O 2 – ) and sterol lipids (m/z – 311.16 C 20 H 23 O 3 – ). ToF-SIMS spectral, imaging, and depth profiling analyses showed that the glass rich in silica and other light elements (“granite glass”) had more “corrosion related” peaks than the glass that was less silica-rich and contained more iron (“dike glass”). Furthermore, these surface and interface compositional and spatial differences observed in the mass spectra and imaging were attributed to bacterial metabolism and an electron transfer mechanism influenced by morphological and compositional differences between the two types of glasses. ToF-SIMS is effective in studying microbial effects, bringing new molecular insights into MIC in a broader context of materials degradation.

Amorphous materials↗
DOE OSTI2023

Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge

Nitrate (NO 3 – ) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO 3 – leaching outcomes. We combine natural dual isotopes of NO 3 – ( 15 N/ 14 N and 18 O/ 16 O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO 3 – leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0–10 cm), with a 12–25-fold increase of 15 N–NO 3 – and 18 O–NO 3 – after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ~80% decline in denitrification activities thereafter. In contrast, deeper soils (60–100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10–20-fold of residual NO 3 – being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO 3 – leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO 3 – changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO 3 – leaching in agroecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Postanaerobic Digestion Manure Fibers as a Renewable Source of Lignin-Derived Aromatic Compounds for Microbial Upgrading

Abstract Postanaerobic digestion manure fibers are an abundant solid residue that remains underutilized. The substantial lignocellulosic content of digested manure opens the possibility of using it as a renewable resource for producing valuable products. In this study, we performed compositional and nuclear magnetic resonance analyses to determine lignin content and aromatic composition of these fibers. Additionally, alkaline-based treatment and reductive catalytic fractionation were evaluated as two different processes to produce aromatic-rich streams. The liquor from the alkaline treatment was subsequently utilized for microbial upgrading to produce 2-pyrone-4,6-dicarboxylic acid (PDC). The results showed that lignin in manure fibers represents 30% of the biomass (dry weight basis), with a ∼26% abundance of β-ether-linked aromatics and ∼13% p-coumarate moieties, indicating that the amount of lignin in the postanaerobic biomass is comparable to a moderately pretreated plant biomass. The alkaline treatment released 5.6 g aromatics/kg fibers, while reductive catalytic fractionation produced 14.0 g aromatics/kg fibers. A bioreactor operated in fed-batch mode produced a yield of ∼1 mol of PDC/mol measured aromatics at a rate of 0.2 g PDC/L·h and a titer of 2.6 g PDC/L. This study demonstrates how postanaerobic digestion manure fibers could be used in a circular bioeconomy by harnessing their lignocellulosic content to extract aromatic compounds and use them for obtaining valuable chemicals via microbial upgrading.

Riascos, Brayan D. [University of Wisconsin-Madiso↗
DOE OSTI2021

Carbon Fluxes and Microbial Activities From Boreal Peatlands Experiencing Permafrost Thaw

Permafrost thaw is occurring in Alaska which may result in a positive feedback to climate warming, due to the release of greenhouse gases such as CO 2 and CH 4 from soils. Here we examined greenhouse gas production along a gradient of “time since thaw,” hypothesizing that fluxes and microbial activities would be highest soon after thaw, and then decline. We observed highest rates of microbial activities, particularly methanogenesis, soon after thaw, coinciding with less decomposed organic matter and higher concentrations of dissolved carbon and nitrogen in soil, possibly of permafrost origin. However, field fluxes were higher in the young thaw site, compared to the older sites, in winter and not summer, a phenomenon that is currently not well understood.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Three-Dimensional Free Gas Flow Focuses Basin-Wide Microbial Methane to Concentrated Methane Hydrate Reservoirs in Geological System

Here, we present a systematic model that links the generation, migration, phase partitioning, and accumulation of methane into a closed loop as the sediment is deposited from the seafloor and buried through the base of hydrate stability zone (BHSZ). In our model, methane is generated by biodegradation of organic carbon in muds. Hydrate does not form and methane is not trapped until a coarse-grained layer is deposited, because the small pores prevent hydrate formation in muds. Instead, methane diffuses into sands/silts where methane solidifies into hydrate. As hydrate-bearing sands/silts pass through the BHSZ during sediment burial, methane hydrate dissociates, and releases free gas. The released and the newly generated free gas below the BHSZ concentrates into a vertical/dipping zone with low capillary entry pressure and high permeability and flows upward driven its buoyancy. When free gas reaches the hydrate stability zone (HSZ), capillary forces drive free gas to flow laterally, preferentially enter sands/silts, feed hydrate growth, and elevate hydrate saturation. With three-dimensional focused free gas flow, microbial methane that is generated from a much larger fetch area of the entire basin, both above and below the BHSZ, is concentrated into coarse-grained layers at structural closures for hydrate formation. Our model illustrates how geological evolution, microbial methane generation, and gas flow by buoyancy couple to generate concentrated hydrate deposits in geological system. These insights can be used to explore for high-concentration methane hydrate and are important for understanding the methane budget and carbon cycle under the seafloor.

58 GEOSCIENCES↗
DOE OSTI2022

Microtopography Matters: Belowground CH 4 Cycling Regulated by Differing Microbial Processes in Peatland Hummocks and Lawns

Water table depth and vegetation are key controls of methane (CH 4 ) emissions from peatlands. Microtopography integrates these factors into features called microforms. Microforms often differ in CH 4 emissions, but microform-dependent patterns of belowground CH 4 cycling remain less clearly resolved. Here, to investigate the impact of microtopography on belowground CH 4 cycling, we characterized depth profiles of the community composition and activity of CH 4 -cycling microbes using 16S rRNA amplicon sequencing, incubations, and measurements of porewater CH 4 concentration and isotopic composition from hummocks and lawns at Sallie's Fen in NH, USA. Geochemical proxies of methanogenesis and methanotrophy indicated that microforms differ in dominant microbial CH 4 cycling processes. Hummocks, where water table depth is lower, had higher porewater redox potential (Eh) and higher porewater δ 13 C-CH 4 values in the upper 30 cm than lawns, where water table depth is closer to the peat surface. Porewater δ 13 C-CH 4 and δD-CH 3 D values were highest at the surface of hummocks where the ratio of methanotrophs to methanogens was also greatest. These results suggest that belowground CH 4 cycling in hummocks is more strongly regulated by methanotrophy, while in lawns methanogenesis is more dominant. We also investigated controls of porewater CH 4 chemistry. The ratio of the relative abundance of methanotrophs to methanogens was the strongest predictor of porewater CH 4 concentration and δ 13 C-CH 4 , while vegetation composition had minimal influence. As microbial community composition was strongly influenced by redox conditions but not vegetation, we conclude that water table depth is a stronger control of belowground CH 4 cycling across microforms than vegetation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily

Abstract Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Microbial diversity drives carbon use efficiency in a model soil

Abstract Empirical evidence for the response of soil carbon cycling to the combined effects of warming, drought and diversity loss is scarce. Microbial carbon use efficiency (CUE) plays a central role in regulating the flow of carbon through soil, yet how biotic and abiotic factors interact to drive it remains unclear. Here, we combine distinct community inocula (a biotic factor) with different temperature and moisture conditions (abiotic factors) to manipulate microbial diversity and community structure within a model soil. While community composition and diversity are the strongest predictors of CUE, abiotic factors modulated the relationship between diversity and CUE, with CUE being positively correlated with bacterial diversity only under high moisture. Altogether these results indicate that the diversity × ecosystem-function relationship can be impaired under non-favorable conditions in soils, and that to understand changes in soil C cycling we need to account for the multiple facets of global changes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

ATP biosensor reveals microbial energetic dynamics and facilitates bioproduction

Adenosine-5’-triphosphate (ATP), the primary energy currency in cellular processes, drives metabolic activities and biosynthesis. Despite its importance, understanding intracellular ATP dynamics’ impact on bioproduction and exploiting it for enhanced bioproduction remains largely unexplored. Here, we harness an ATP biosensor to dissect ATP dynamics across different growth phases and carbon sources in multiple microbial strains. We find transient ATP accumulations during the transition from exponential to stationary growth phases in various conditions, coinciding with fatty acid (FA) and polyhydroxyalkanoate (PHA) production in Escherichia coli and Pseudomonas putida, respectively. We identify carbon sources (acetate for E. coli, oleate for P. putida) that elevate steady-state ATP levels and boost FA and PHA production. Moreover, we employ ATP dynamics as a diagnostic tool to assess metabolic burden, revealing bottlenecks that limit limonene bioproduction. Our results not only elucidate the relationship between ATP dynamics and bioproduction but also showcase its value in enhancing bioproduction in various microbial species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades

With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Missing microbial eukaryotes and misleading meta-omic conclusions

Meta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the crucial importance of database completeness and curation in enabling accurate environmental interpretation. We show that taxonomic membership of sequence clusters estimates community composition more accurately than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and selecting and evaluating these databases is a critical part of correctly annotating protistan taxonomy in environmental datasets. We argue that ongoing curation of genetic resources is crucial in accurately annotating protists in in situ meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Bioadaptive Ni single atoms unlock high rate microbial electrosynthesis of isopropanol from CO 2

Hybrid systems that integrate electrochemical CO 2 reduction with microbial upgrading offer a viable route to high value organic compounds from CO 2 at ambient conditions. However, electrocatalyst deactivation in microbial growth media remains a key barrier, limiting efficiency and increasing cost. Here we show that a bioadaptive single-atom nickel catalyst (Ni SAC), coupled with genetically engineered Clostridium ljungdahlii, enables robust electrosynthesis of isopropanol (IPA) from CO 2 via a CO-mediated pathway. Instead of relying on H 2 as an electron carrier, the system applies high-rate CO formation in complex growth media, maintaining a tunable CO Faradaic efficiency up to 92%, which is 9.4 to 52.7 times greater than conventional Ag catalysts. This performance supports stable IPA production at current density of 10.8 A/m 2 and production rate of 161.3 mg/L/day. In situ Raman and X-ray absorption spectroscopy, together with theoretical calculations, indicate that the Ni SAC can resist competing organic adsorption and retain its coordination structure during CO 2 reduction in bioelectrolytes, providing a mechanistic basis for the catalyst stability and integrated process performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A soil-inspired dynamically responsive chemical system for microbial modulation

Interactions between the microbiota and their colonized environments mediate critical pathways from biogeochemical cycles to homeostasis in human health. Here, in this study, we report a soil-inspired chemical system that consists of nanostructured minerals, starch granules and liquid metals. Fabricated via a bottom-up synthesis, the soil-inspired chemical system can enable chemical redistribution and modulation of microbial communities. We characterize the composite, confirming its structural similarity to the soil, with three-dimensional X-ray fluorescence and ptychographic tomography and electron microscopy imaging. We also demonstrate that post-synthetic modifications formed by laser irradiation led to chemical heterogeneities from the atomic to the macroscopic level. The soil-inspired material possesses chemical, optical and mechanical responsiveness to yield write-erase functions in electrical performance. The composite can also enhance microbial culture/biofilm growth and biofuel production in vitro. Finally, we show that the soil-inspired system enriches gut bacteria diversity, rectifies tetracycline-induced gut microbiome dysbiosis and ameliorates dextran sulfate sodium-induced rodent colitis symptoms within in vivo rodent models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats

Abstract Many microbes in nature reside in dense, metabolically interdependent communities. We investigated the nature and extent of microbe-virus interactions in relation to microbial density and syntrophy by examining microbe-virus interactions in a biomass dense, deep-sea hydrothermal mat. Using metagenomic sequencing, we find numerous instances where phylogenetically distant (up to domain level) microbes encode CRISPR-based immunity against the same viruses in the mat. Evidence of viral interactions with hosts cross-cutting microbial domains is particularly striking between known syntrophic partners, for example those engaged in anaerobic methanotrophy. These patterns are corroborated by proximity-ligation-based (Hi-C) inference. Surveys of public datasets reveal additional viruses interacting with hosts across domains in diverse ecosystems known to harbour syntrophic biofilms. We propose that the entry of viral particles and/or DNA to non-primary host cells may be a common phenomenon in densely populated ecosystems, with eco-evolutionary implications for syntrophic microbes and CRISPR-mediated inter-population augmentation of resilience against viruses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Machine learning sheds light on microbial dark proteins

In this article, metagenomics projects have revealed more than 8 billion non-redundant microbial protein sequences from across the Earth’s biosphere. Of these, 1.17 billion proteins do not have recognizable homologues in any of the more than 100,000 reference genomes available1. Understanding the function of these microbial proteins is a daunting task. Fortunately, machine learning has recently achieved unprecedented accuracy in modelling complex biological data and making predictions. At the forefront of these advancements are machine learning-based approaches that can confidently predict atomic-level protein structures for many (but not all) amino acid sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microbial secondary metabolites: advancements to accelerate discovery towards application

Microbial secondary metabolites not only have key roles in microbial processes and relationships but are also valued in various sectors of today’s economy, especially in human health and agriculture. The advent of genome sequencing has revealed a previously untapped reservoir of biosynthetic capacity for secondary metabolites indicating that there are new biochemistries, roles and applications of these molecules to be discovered. New predictive tools for biosynthetic gene clusters (BGCs) and their associated pathways have provided insights into this new diversity. Advanced molecular and synthetic biology tools and workflows including cell-based and cell-free expression facilitate the study of previously uncharacterized BGCs, accelerating the discovery of new metabolites and broadening our understanding of biosynthetic enzymology and the regulation of BGCs. These are complemented by new developments in metabolite detection and identification technologies, all of which are important for unlocking new chemistries that are encoded by BGCs. This renaissance of secondary metabolite research and development is catalysing toolbox development to power the bioeconomy.

Dinglasan, Jaime Lorenzo N↗