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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS1983

Fungi and bacteria involved in desert varnish formation

Desert varnish is a coating of ferromanganese oxides and clays that develops on rock surfaces in arid to semi-arid regions. Active respiration but not photosynthesis was detected on varnished rock surfaces from the Sonoran Desert. Light microscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations, and cultivation experiments indicate that both fungi, primarily dematiaceous hyphomycetes, and bacteria are found on and within desert varnish coatings from the arid regions studied. Some fungi grow as microcolonial fungi (MCF) on rocks, and microscopic observations suggest MCF become incorporated in the varnish coating. SEM-EDAX (energy dispersive X-ray systems) analyses indicate the MCF contain 3 of the characteristic elements of varnish: iron, aluminum, and silicon. In some locations, MCF are also enriched in manganese relative to the rock substratum. Furthermore, some of the dematiaceous hyphomycetes that have been cultivated are able to oxidize manganese under laboratory conditions. It is possible that manganese-oxidizing bacteria, which are found in varnish, also play an important role in varnish formation.

Taylor-George, S.↗
NASA NTRS2019

MycoMaterials: Metal-Fungi Hybrids

There is an interest in creating aerospace structures that regenerate, communicate and that are capable of using carbondioxide as a fuel source. Before such a vision is achieved several fundamental questions must first be answered. For example, what are the optimal conditions and laboratory settings for mycelium growth and is it possible for mycelium to digest different metals to form metal-mycelium hybrid structures? Recent research has shown that fungi and photosynthetic organisms can absorb harmful metals. Eight different species of fungi were grown such as blue oyster (Pleurotus columbinus), reishi ling chi (Ganoderma lucidum), and shaggy mane (Coprinus comatus). Species of fungi were chosen based on their potential growth rate, potential strength and non-toxicity to humans. Metal-mycelium hybrids were developed by using both the cell and mycelium life stages. In experiments involving the mycelium stage, varying amounts of sterilized sawdust (0.5-1g), zinc sulfide (0.5-1g), and small pieces of aluminum foil (0.1-1g) were applied on top of the mycelium growing on petri dishes. For experiments using the cell stage, 8-9 drops of the fungal sample were applied to zinc sulfide (0.5-1g) and aluminum foil (0.5-1g). Mycelium (blue oyster) were grown on to differing quantities of aluminum foil. Cells (shaggy mane) have been grown onto aluminum foil with and without nutrients from the petri dish. Shaggy mane cells have also grown onto 0.5 g of zinc sulfide.

Kyles-Stewart, Maiya A.↗
DOE OSTI2021

Effect of Cultivation Conditions on the Bioconversion of 4-Hydroxybenzoic Acid in Two White-Rot Fungi

White-rot fungi (WRF) are the most efficient organisms for lignin degradation in nature. A recent study has also shown the ability of WRF in funneling lignin-derived aromatics, including 4-hydroxybenzoic acid (4HBA) and vanillic acid, to central metabolism. However, it is unknown how the cultivation conditions affect the conversion of lignin-derived aromatic compounds. To address this, we performed multi-omic analyses and tracked the conversion of 4HBA in different cultivation conditions in two white-rot fungi: Trametes versicolor and Ceriporiopsis subvermispora. Specifically, we evaluated the effect of static and agitation cultivation conditions in the absence and the presence of antioxidants on fungal performance. We found that the comparison between static and agitation has the higher number of differentially expressed genes or protein abundances at the transcriptomic and proteomic levels, respectively, compared to the presence or the absence of antioxidants. Gene mapping on the enzymatic steps of the proposed 4HBA conversion pathway revealed that agitation causes upregulation of several oxidase genes such as aldehyde dehydrogenases, aldehyde oxidases, and hydroxylases in both fungi. Time-course experiments including 4HBA and cellobiose as carbon sources showed that T. versicolor exhibited higher 4HBA conversion levels in agitation (~110% more conversion, compared to static cultivation conditions) and in the presence of antioxidants (~10% more conversion, compared to the treatments without antioxidants). Interestingly, these trends were not found in C. subvermispora, suggesting different carbon metabolism in both species. Our findings are fundamental to better understand carbon sequestration from lignin in WRF, which will be key for future applications in the lignin valorization field.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

From the bench to the reactor: engineered filamentous fungi for biochemical and biomaterial production

Filamentous fungi can convert a wide variety of naturally occurring chemical compounds, including organic biomass and waste streams, into a range of products. They have long been used for industrial organic acid production and food preparation. In this review, we will discuss production of products such as organic acids, lipids, small molecules, enzymes, materials, and foods, and highlight advances in metabolic and protein engineering, including CRISPR-Cas9-mediated strain improvements. We discuss to what extent these products are already being made on a commercial scale, as well as what is still required to make certain promising concepts industrially and commercially relevant. Despite significant progress, the systematic application of synthetic biology to filamentous fungi remains in its infancy, with many opportunities for discovery and innovation as new strains and genetic tools are developed. The integration of fungal biotechnology into circular and bio-based economies promises to address critical challenges in waste management, resource sustainability, and the development of new materials for terrestrial and extraterrestrial applications, but requires further developments in genetic engineering and process design.

09 BIOMASS FUELS↗
DOE OSTI2022

Cross-Kingdom Comparative Genomics of Aromatic Catabolic Pathways in Fungi and Bacteria

The overall goal of this project is to test the hypothesis that white-rot fungi can simultaneously depolymerize lignin extracellularly and catabolize depolymerization products intracellularly as carbon and energy sources. The results from this project will lead to improved understanding of lignin utilization by white-rot fungi, and enable identification of promising fungal strains for lignin catabolism and valorization. As part of this effort, we have conducted a comparative genomic study to investigate a diversity of aromatic catabolic pathways in the fungal and bacterial kingdoms. Furthermore, we have combined genomic and phylogenetic approaches to decipher the evolution of certain aromatic catabolic enzymes and discover new classes of enzymes, which represents a foundation for future biochemical and molecular genetic studies.

aromatic compounds↗
DOE OSTI2023

Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi

Abstract Membrane‐embedded transporters impart essential functions to cells as they mediate sensing and the uptake and extrusion of nutrients, waste products, and effector molecules. Promiscuous multidrug exporters are implicated in resistance to drugs and antibiotics and are highly relevant for microbial engineers who seek to enhance the tolerance of cell factory strains to hydrophobic bioproducts. Here, we report on the identification of small multidrug resistance (SMR) transporters in early‐branching anaerobic fungi (Neocallimastigomycetes). The SMR class of transporters is commonly found in bacteria but has not previously been reported in eukaryotes. In this study, we show that SMR transporters from anaerobic fungi can be produced heterologously in the model yeast Saccharomyces cerevisiae , demonstrating the potential of these proteins as targets for further characterization. The discovery of these novel anaerobic fungal SMR transporters offers a promising path forward to enhance bioproduction from engineered microbial strains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Nitrogen Fertilizer, Arbuscular Mycorrhizal Fungi, and Soil Nematodes Affect Lignin Quality and Quantity in Switchgrass (Panicum virgatum L.)

Plant lignin content and composition, which limit cell wall digestibility and efficiency of cellulose conversion to bioethanol, can be influenced by belowground biotic and abiotic factors. Switchgrass (Panicum virgatum L.) is a leading lignocellulosic biofuel crop and forms strong belowground associations with arbuscular mycorrhizal fungi (AMF), is susceptible to belowground plant-parasitic nematodes (PPN), and when grown in monoculture generally requires nitrogen (N) fertilization. The main objectives of the study were to investigate the effects of N fertilizer and belowground organisms on lignin content and composition of switchgrass. Here, leaf, stem, and root tissues were evaluated separately to test whether these factors had varying belowground (local) or aboveground (systemic) effects on plants. These factors were manipulated in a field study in 2017 using biocide applications to reduce soil fungi and nematodes. Combined biocide application reduced p-hydroxyphenyl (H) unit abundance in the leaves by 14% and increased the syringyl:guaiacyl (S:G) ratio in stems by 2%. Application of fungicide alone increased stem syringyl (S) unit by 12.4% as compared with control plots, and 11.1% as compared with nematicide plots. Overall, fertilizer increased total stem lignin by 3%, stem S unit by 6.7%, and stem S:G ratio by 10%, whereas it reduced the amount of H-unit in the roots by 11%. While the effects of N fertilizer were more pronounced in this study, changes to soil organisms had similar magnitudes of effect for some measures of lignin, indicating that these belowground interactions may be important for growers to consider in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Biofilm disruption enhances growth rate and carbohydrate-active enzyme production in anaerobic fungi

Anaerobic gut fungi (AGF) are lignocellulose degraders that naturally form biofilms in the rumen of large herbivores and in standard culture techniques. While biofilm formation enhances biomass degradation and carbohydrate-active enzyme (CAZyme) production in some bacteria and aerobic fungi, gene expression and metabolism in AGF biofilms have not been compared to non-biofilm cultures. Here, using the tunable morphology of the non-rhizoidal AGF, Caecomyces churrovis, the impacts of biofilm formation on AGF gene expression, metabolic flux, growth rate, and xylan degradation rate are quantified to inform future industrial scale-up efforts. Contrary to previous findings, C. churrovis upregulated catabolic CAZymes in stirred culture relative to biofilm culture. Using a de novo transcriptome, 197 new transcripts with predicted CAZyme function were identified. Stirred cultures grew and degraded xylan significantly faster than biofilm-forming cultures with negligible differences in primary metabolic flux, offering a way to accelerate AGF biomass valorization without altering the fermentation product profile. The rhizoidal AGF, Neocallimastix lanati, also grew faster with stirring on a solid plant substrate, suggesting that the advantages of stirred C. churrovis cultures may apply broadly to other AGF.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi

Sesquiterpene cyclases (STC) catalyse the cyclization of the C15 molecule farnesyl diphosphate into a vast variety of mono- or polycyclic hydrocarbons and, for a few enzymes, oxygenated structures, with diverse stereogenic centres. The huge diversity in sesquiterpene skeleton structures in nature is primarily the result of the type of cyclization driven by the STC. Despite the phenomenal impact of fungal sesquiterpenes on the ecology of fungi and their potentials for applications, the fungal sesquiterpenome is largely untapped. The identification of fungal STC is generally based on protein sequence similarity with characterized enzymes. This approach has improved our knowledge on STC in a few fungal species, but it has limited success for the discovery of distant sequences. Besides, the tools based on secondary metabolite biosynthesis gene clusters have shown poor performance for terpene cyclases. Here, we used four sets of sequences of fungal STC that catalyse four types of cyclization, and specific amino acid motives to identify phylogenetically related sequences in the genomes of basidiomycetes fungi from the order Polyporales. We validated that four STC genes newly identified from the genome sequence of Leiotrametes menziesii, each classified in a different phylogenetic clade, catalysed a predicted cyclization of farnesyl diphosphate. We built HMM models and searched STC genes in 656 fungal genomes genomes. We identified 5605 STC genes, which were classified in one of the four clades and had a predicted cyclization mechanism. We noticed that the HMM models were more accurate for the prediction of the type of cyclization catalysed by basidiomycete STC than for ascomycete STC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A large-scale screening campaign of putative carbohydrate-active enzymes reveals a novel xylanase from anaerobic gut fungi

The genomes of anaerobic gut fungi (AGF) encode a diverse array of carbohydrate-active enzymes (CAZymes), yet exceedingly few of these enzymes have been experimentally validated or expressed in heterologous systems. Here, we developed a predictive bioinformatic pipeline to annotate novel putative CAZymes from anaerobic fungi and validate their activity through large-scale heterologous expression in Escherichia coli. A total of 173 fungal proteins from Piromyces finnis associated with biomass degradation were synthesized and expressed in E. coli, and 9.8% were soluble with expression levels exceeding 5% of the total proteome using high-throughput proteomic screening. Among these 17 heterologously expressed proteins, analysis with AlphaFold and FoldSeek predicted 13 multi-functional proteins containing catalytic domains fused with repetitive fungal dockerins, and half of the substrate predictions were experimentally validated. One promising enzyme, celsome_012, exhibited robust and specific activity against beechwood xylan at 37°C and pH 6.4, with titers that were also fivefold higher than those of other recombinant proteins screened here. Both Michaelis-Menten kinetics and the linearized Lineweaver-Burk equation yielded consistent values for K m , and its activation energy was estimated at 51.9 kJ/mol based on the Arrhenius model. This work supports the industrial translation of anaerobic fungal CAZymes due to their robust lignocellulolytic activity and provides a framework for prioritizing AGF proteins for efficient E. coli heterologous expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi

Within the forest community, competition and facilitation between adjacent-growing conspecific and heterospecific plants are mediated by interactions involving common mycorrhizal networks. The ability of plants to alter their neighbor’s microbiome is well documented, but the molecular biology of plant-fungal interactions during competition and facilitation has not been previously examined. We used a common soil-plant bioassay experiment to study molecular plant-microbial interactions among rhizosphere communities associated with Pinus taeda (native host) and Populus trichocarpa (non-native host). Gene expression of interacting fungal and bacterial rhizosphere communities was compared among three plant-pairs: Populus growing with Populus , Populus with Pinus , and Pinus with Pinus . Our results demonstrate that heterospecific plant partners affect the assembly of root microbiomes, including the changes in the structure of host specific community. Comparative metatranscriptomics reveals that several species of ectomycorrhizal fungi (EMF) and saprotrophic fungi exhibit different patterns of functional and regulatory gene expression with these two plant hosts. Heterospecific plants affect the transcriptional expression pattern of EMF host-specialists (e.g., Pinus -associated Suillus spp.) on both plant species, mainly including the genes involved in the transportation of amino acids, carbohydrates, and inorganic ions. Alteration of root microbiome by neighboring plants may help regulate basic plant physiological processes via modulation of molecular functions in the root microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Biochemical and structural characterization of enzymes in the 4-hydroxybenzoate catabolic pathway of lignin-degrading white-rot fungi

White-rot fungi (WRF) are the most efficient lignin-degrading organisms in nature. However, their capacity to use lignin-related aromatic compounds, such as 4-hydroxybenzoate, as carbon sources has only been described recently. Previously, the hydroxyquinol pathway was proposed for the bioconversion of these compounds in fungi, but gene- and structure-function relationships of the full enzymatic pathway remain uncharacterized in any single fungal species. Here, we characterize seven enzymes from two WRF, Trametes versicolor and Gelatoporia subvermispora, which constitute a four-enzyme cascade from 4-hydroxybenzoate to β-ketoadipate via the hydroxyquinol pathway. Furthermore, we solve the crystal structure of four of these enzymes and identify mechanistic differences with the closest bacterial and fungal structural homologs. Overall, this research expands our understanding of aromatic catabolism by WRF and establishes an alternative strategy for the conversion of lignin-related compounds to the valuable molecule β-ketoadipate, contributing to the development of biological processes for lignin valorization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The effects of mixed-species root zones on the resistance of soil bacteria and fungi to long-term experimental and natural reductions in soil moisture

Mixed forest stands tend to be more resistant to drought than species-specific stands partially due to complementarity in root ecology and physiology. For this work, we asked whether complementary differences in the drought resistance of soil microbiomes might contribute to this phenomenon. We experimented on the effects of reduced soil moisture on bacterial and fungal community composition in species-specific (single species) and mixed-species root zones of Norway spruce and European beech forests in a 5-year-old throughfall-exclusion experiment and across seasonal (spring-summer-fall) and latitudinal moisture gradients. Bacteria were most responsive to changes in soil moisture, especially members of Rhizobiales, while fungi were largely unaffected, including ectomycorrhizal fungi (EMF). Community resistance was higher in spruce relative to beech root zones, corresponding with the proportions of drought-favored (more in spruce) and drought-sensitive bacterial taxa (more in beech). The spruce soil microbiome also exhibited greater resistance to seasonal changes between spring (wettest) and fall (driest). Mixed-species root zones contained a hybrid of beech- and spruce-associated microbiomes. Several bacterial populations exhibited either enhanced resistance or greater susceptibility to drought in mixed root zones. Overall, patterns in the relative abundances of soil bacteria closely tracked moisture in seasonal and latitudinal precipitation gradients and were more predictive of soil water content than other environmental variables. We conclude that complementary differences in the drought resistance of soil microbiomes can occur and the likeliest form of complementarity in mixed-root zones coincides with the enrichment of drought-tolerant bacteria associated with spruce and the sustenance of EMF by beech.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Study of wrap mode impact on Pseudomonas aeruginosa motion in the chemotactic field of fungi

An agent-based discrete computational model biologically calibrated to Pseudomonas aeruginosa migration is used to explore the impacts of bacterial reversals and wrap mode on the efficiency of motion in different environments, both with and without chemotaxis. It is first shown that wrap mode increases the exploration of continuous multimodal chemotactic profiles such as those produced by biologically relevant fungal networks. For cells undergoing a run-reverse pattern, it is shown that the bacteria are likely to remain at the first local chemoattractant maximal production site on a hypha they find. However, with wrap mode, the bacteria can more easily escape these local sites to further explore their neighboring environment along the fungi, suggesting that wrap mode may be beneficial for migration along the fungi in liquid. In a different set of simulations of bacterial motion close to an isolated chemotactic source, wrap mode is shown to increase the ability of a bacterium to reorient toward the source while reducing the overall motion required for similar chemotactic efficiency as a run-reverse strategy, suggesting a potential metabolic benefit. In contrast, model simulations show that wrap mode can increase the rate of dispersal of P. aeruginosa in a nonchemotactic environment.

Hansen, Austin [University of California, Riversid↗
DOE OSTI2023

Benefits of symbiotic ectomycorrhizal fungi to plant water relations depend on plant genotype in pinyon pine

Rhizosphere microbes, such as root-associated fungi, can improve plant access to soil resources, affecting plant health, productivity, and stress tolerance. While mycorrhizal associations are ubiquitous, plant–microbe interactions can be species specific. Here we show that the specificity of the effects of microbial symbionts on plant function can go beyond species level: colonization of roots by ectomycorrhizal fungi (EMF) of the genus Geopora has opposite effects on water uptake, and stomatal control of desiccation in drought tolerant and intolerant genotypes of pinyon pine (Pinus edulis Engelm.). These results demonstrate, for the first time, that microorganisms can have significant and opposite effects on important plant functional traits like stomatal control of desiccation that are associated with differential mortality and growth in nature. They also highlight that appropriate pairing of plant genotypes and microbial associates will be important for mitigating climate change impacts on vegetation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Microevolution in the pansecondary metabolome of Aspergillus flavus and its potential macroevolutionary implications for filamentous fungi

Significance Secondary metabolites (SMs) produced by fungi mediate ecological interactions, define fungal niches, and are of profound pharmacological importance to humans. Most work on SMs has focused on a small number of individuals from each species, not fully reflecting the importance of intraspecific diversity. We demonstrate that even in one of the best-studied model fungi, the carcinogen-producing Aspergillus flavus , more than 25% of SM-producing biosynthetic gene clusters (BGCs) are novel and/or show population-specific variants. These results support the finding that the organization of BGC diversity into population-specific patterns may sometimes result from ecologically important interactions and may inform evolutionary and etiological inferences of SM capacities within a species. Importantly, our work also presents a vision of sources of potential pharmaceuticals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism

Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter.

59 BASIC BIOLOGICAL SCIENCES↗