Search NASA⌕ Search

SEARCH · Search NASA

Results for “fungal biology”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
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 OSTI2023

Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi

Intimate associations between fungi and intracellular bacterial endosymbionts are becoming increasingly well understood. Phylogenetic analyses demonstrate that bacterial endosymbionts of Mucoromycota fungi are related either to free-living Burkholderia or Mollicutes species. The so-called Burkholderia-related endosymbionts or BRE comprise Mycoavidus, Mycetohabitans and Candidatus Glomeribacter gigasporarum. These endosymbionts are marked by genome contraction thought to be associated with intracellular selection. However, the conclusions drawn thus far are based on a very small subset of endosymbiont genomes, and the mechanisms leading to genome streamlining are not well understood. The purpose of this study was to better understand how intracellular existence shapes Mycoavidus and BRE functionally at the genome level. To this end we generated and analyzed 14 novel draft genomes for Mycoavidus living within the hyphae of Mortierellomycotina fungi. We found that our novel Mycoavidus genomes were significantly reduced compared to free-living Burkholderiales relatives. Using a genome-scale phylogenetic approach including the novel and available existing genomes of Mycoavidus, we show that the genus is an assemblage composed of two independently derived lineages including three well supported clades of Mycoavidus. Using a comparative genomic approach, we shed light on the functional implications of genome reduction, documenting shared and unique gene loss patterns between the three Mycoavidus clades. We found that many endosymbiont isolates demonstrate patterns of vertical transmission and host-specificity, but others are present in phylogenetically disparate hosts. We discuss how reductive evolution and host specificity reflect convergent adaptation to the intrahyphal selective landscape, and commonalities of eukaryotic endosymbiont genome evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi

With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world’s most economically damaging agricultural diseases. Despite P. pachyrhizi’s impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Machine learning reveals genes impacting oxidative stress resistance across yeasts

Reactive oxygen species (ROS) are highly reactive molecules encountered by yeasts during routine metabolism and during interactions with other organisms, including host infection. Here, we characterize the variation in resistance to the ROS-inducing compound tert -butyl hydroperoxide across the ancient yeast subphylum Saccharomycotina and use machine learning (ML) to identify gene families whose sizes are predictive of ROS resistance. The most predictive features are enriched in gene families related to cell wall organization and include two reductase gene families. We estimate the quantitative contributions of features to each species’ classification to guide experimental validation and show that overexpression of the old yellow enzyme (OYE) reductase increases ROS resistance in Kluyveromyces lactis , while Saccharomyces cerevisiae mutants lacking multiple mannosyltransferase-encoding genes are hypersensitive to ROS. Altogether, this work provides a framework for how ML can uncover genetic mechanisms underlying trait variation across diverse species and inform trait manipulation for clinical and biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae . A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S . cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S . cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum . Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae . The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S . cerevisiae .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Loosenin-Like Proteins from Phanerochaete carnosa Impact Both Cellulose and Chitin Fiber Networks

The present study deepens investigations of microbial expansin-related proteins and their applied significance by (i) reporting a detailed comparison of diverse loosenins encoded by the same organism, (ii) considering both cellulosic and chitin-containing materials as targeted substrates, and (iii) investigating the impact of the C-terminal carbohydrate binding module (CBM) present in other expansin-related proteins on loosenin function. By revealing the potential of fungal loosenins to impact both cellulose and chitin-containing networks, our study reveals a possible biological and applied role of loosenins in fungal cell wall processing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A centralized resource for bacterial–fungal interactions research

Research on bacterial-fungal interactions (BFIs) has revealed that fungi and bacteria frequently interact with one another within diverse ecosystems and microbiomes. Assessing the current state of knowledge within the field of BFI research, particularly with respect to what interactions between bacteria and fungi have been previously described, is very challenging and time consuming. This is largely due to a lack of any centralized resource, with reports of BFIs being spread across publications in numerous journals using non-standardized text to describe the relationships. To address this issue, we have developed the BFI Research Portal, a publicly accessible database of previously reported interactions between bacterial and fungal taxa to serve as a centralized resource for the field. Users can query bacterial or fungal taxa to see what members from the other kingdom have been observed as interaction partners. Search results are accompanied by interactive and intuitive visual outputs, and the database is a dynamic resource that will be updated as new BFIs are reported.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Widespread bacterial diversity within the bacteriome of fungi

Abstract Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number and diversity of examinations have increased, but current knowledge is predominantly limited to a small number of fungal taxa and bacterial partners. Here, we screened for potential bacterial associates in over 700 phylogenetically diverse fungal isolates, representing 366 genera, or a tenfold increase compared with previously examined fungal genera, including isolates from several previously unexplored phyla. Both a 16 S rDNA-based exploration of fungal isolates from four distinct culture collections spanning North America, South America and Europe, and a bioinformatic screen for bacterial-specific sequences within fungal genome sequencing projects, revealed that a surprisingly diverse array of bacterial associates are frequently found in otherwise axenic fungal cultures. We demonstrate that bacterial associations with diverse fungal hosts appear to be the rule, rather than the exception, and deserve increased consideration in microbiome studies and in examinations of microbial interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Trade-Offs Between Growth Rate and Other Fungal Traits

If we better understand how fungal responses to global change are governed by their traits, we can improve predictions of fungal community composition and ecosystem function. Specifically, we can examine trade-offs among traits, in which the allocation of finite resources toward one trait reduces the investment in others. We hypothesized that trade-offs among fungal traits relating to rapid growth, resource capture, and stress tolerance sort fungal species into discrete life history strategies. We used the Biolog Filamentous Fungi database to calculate maximum growth rates of 37 fungal species and then compared them to their functional traits from the fun fun database. In partial support of our hypothesis, maximum growth rate displayed a negative relationship with traits related to resource capture. Moreover, maximum growth rate displayed a positive relationship with amino acid permease, forming a putative Fast Growth life history strategy. A second putative life history strategy is characterized by a positive relationship between extracellular enzymes, including cellobiohydrolase 6, cellobiohydrolase 7, crystalline cellulase AA9, and lignin peroxidase. These extracellular enzymes were negatively related to chitosanase 8, an enzyme that can break down a derivative of chitin. Chitosanase 8 displayed a positive relationship with many traits that were hypothesized to cluster separately, forming a putative Blended life history strategy characterized by certain resource capture, fast growth, and stress tolerance traits. These trait relationships complement previously explored microbial trait frameworks, such as the Competitor-Stress Tolerator-Ruderal and the Yield-Resource Acquisition-Stress Tolerance schemes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Variation in hyphal production rather than turnover regulates standing fungal biomass in temperate hardwood forests

Abstract Soil fungi link above‐ and belowground carbon (C) fluxes through their interactions with plants and contribute to C and nutrient dynamics through the production, turnover, and activity of fungal hyphae. Despite their importance to ecosystem processes, estimates of hyphal production and turnover rates are relatively uncommon, especially in temperate hardwood forests. We sequentially harvested hyphal ingrowth bags to quantify the rates of Dikarya (Ascomycota and Basidiomycota) hyphal production and turnover in three hardwood forests in the Midwestern United States, where plots differed in their abundance of arbuscular (AM)‐ vs. ectomycorrhizal (ECM)‐associated trees. Hyphal production rates increased linearly with the percentage of ECM trees and annual production rates were 66% higher in ECM‐ than AM‐dominated plots. Hyphal turnover rates did not differ across the mycorrhizal gradient (plots varying in their abundance of AM vs. ECM trees), suggesting that the greater fungal biomass in ECM‐dominated plots relates to greater fungal production rather than slower fungal turnover. Differences in hyphal production across the gradient aligned with distinctly different fungal communities and activities. As ECM trees increased in dominance, fungi inside ingrowth bags produced more extracellular enzymes involved in degrading nitrogen (N)‐bearing relative to C‐bearing compounds, suggesting greater fungal (and possibly plant) N demand in ECM‐dominated soils. Collectively, our results demonstrate that shifts in temperate tree species composition that result in changes in the dominant type of mycorrhizal association may have strong impacts on Dikarya hyphal production, fungal community composition and extracellular enzyme activity, with important consequences for soil C and N cycling.

59 BASIC BIOLOGICAL SCIENCES↗
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↗
NASA NTRS2017

Characterization of Biological Fallout Particles of Cleanrooms to Measure Spacecraft Cleanliness

NASA cleanrooms are humidity, temperature-regulated, and particle contaminant-controlled environments used for spacecraft assembly. Microorganisms, which are crucial contaminants shed from humans and transported through the environment, can adapt to the oligotrophic cleanroom conditions. These biogenic particles need to be identified to extend our knowledge of biological contamination for future NASA mission use. Here, we devised an aluminum coupon with polycarbonate filter setup to collect fallout particles from an ISO 5 and an ISO 7 cleanroom. We demonstrated the presence of microbial particles, as standalone entities and associated with inert particles in cleanroom environments. The contamination was confirmed as biogenic in virtue of estimating the elemental composition of individual and aggregated particles using an epifluorescence and Field Emission Scanning Electron Microscopy (FESEM) coupled with an energy dispersive X-ray analysis (EDX). Epifluorescence microscopy showed that the particles were stained less (25%) with SYTO 9 and more (75%) with propidium iodide, suggesting that the suspected biogenic particles are membrane-compromised. Remarkably, biological particles such as bacteria and fungal spores/hyphae were observed at sizes ranging from 2 to 70 µm, with abundant C and O elemental signatures and essential tracers (Na, Mg, K, Ca and Cl). Inert particles (2 to 500 µm) that were characterized included compositions such as silica (SiO2), aluminosilicates (Al, Si), and carbonaceous fibers. Furthermore, we designed and illustrated a unique correlative epifluorescence and FE-SEM method to strengthen this approach by acquiring the same biogenic particles in the same filter coupon for a one-to-one comparison. Interestingly, the SYTO 9 stained particles showed abundant C and O elemental signature implying that they are viable microbial particles. Constant evaluation of cleanroom biological and inert particles will help to characterize biological contamination for future NASA missions (e.g. Mars 2020).

Malli Mohan, Ganesh Babu↗
DOE OSTI2024

Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit

Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and demonstrated use cases for bioengineered food production by edible strains are lacking. Here, we develop a modular synthetic biology toolkit for Aspergillus oryzae, an edible fungus used in fermented foods, protein production, and meat alternatives. Our toolkit includes a CRISPR-Cas9 method for gene integration, neutral loci, and tunable promoters. We use these tools to elevate intracellular levels of the nutraceutical ergothioneine and the flavor-and color molecule heme in the edible biomass. The strain overproducing heme is red in color and is readily formulated into imitation meat patties with minimal processing. These findings highlight the promise of synthetic biology to enhance fungal foods and provide useful genetic tools for applications in food production and beyond.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Spatial scales of competition and a growth–motility trade-off interact to determine bacterial coexistence

The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth–motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth–motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Biodiversity and disease risk in an algal biofuel system: An experimental test in outdoor ponds using a before-after-control-impact (BACI) design

For outdoor cultivation of algal feedstocks to become a commercially viable and sustainable option for biofuel production, algal cultivation must maintain high yields and temporal stability in environmentally variable outdoor ponds. One of the main challenges is mitigating disease outbreaks that leads to culture crashes. Drawing on predictions from the ‘dilution effect’ hypothesis, in which increased biodiversity is thought to reduce disease risk in a community, a teste of whether algal polycultures would reduce disease risk and improve feedstock production efficiencies compared to monocultures was performed. While the positive benefits of biodiversity on disease risk have been demonstrated in various systems, to the best of our knowledge this is the first test in an algal biofuel system. Here, the results a before-after-control-impact (BACI) experimental design to compare mean monoculture (control) and polyculture (impact) yield, stability, and productivity before and after fungal infection when grown in 400-L outdoor raceway ponds are presented. It has been found that polycultures did not experience a reduction in disease risk compared to monocultures or differ in production efficiencies throughout the course of the 43-day experiment. These results show that polyculture feedstocks can maintain similar levels of productivity, stability, and disease resistance to that of a monoculture. Determining whether these results are generalizable or represent one case study requires additional outdoor experiments using a larger variety of host and pathogen species.

09 BIOMASS FUELS↗
DOE OSTI2021

Exosomes derived from thymic stromal lymphopoietin-treated dendritic cells regulate T helper 17/regulatory T cell differentiation via miR-21/Smad7 axis

Highlights: • Exosomes from TSLP-treated DCs promote Th17 differentiation. • Exosomes from TSLP-treated DCs inhibit Tregs differentiation. • MiR-21 is highly expressed in exosomes from TSLP-treated DCs. • Exosomal miR-21 regulates Th17/Treg differentiation by targeting Smad7. Thymic stromal lymphopoietin (TSLP) is associated with fungal keratitis. This work aims to investigate whether TSLP can regulate T helper (Th) 17 and regulatory T cell (Treg) differentiation. We separated dendritic cells (DCs) from peripheral blood of healthy volunteers. DCs were treated with TSLP to activate DCs, and exosomes were obtained. CD{sup +} T cells were incubated with exosomes from TSLP-treated DCs. We found that exosomes from TSLP-treated DCs notably promoted the proportions of Th17 cells and inhibited the proportions of Tregs in the CD4{sup +} T cells. Moreover, exosomes from TSLP-treated DCs enhanced the expression of retinoid-related orphan receptor γt (RORγt) and interleukin 17 (IL-17), and repressed the expression of forkhead box protein P3 (Foxp3) and interleukin 10 (IL-10) in the CD4{sup +} T cells. Furthermore, miR-21 was highly expressed in exosomes from TSLP-treated DCs. Exosomes from TSLP-treated miR-21-silenced DCs promoted Treg differentiation and suppressed Th17 differentiation. Smad7 up-regulation repressed Th17 differentiation and enhanced Treg differentiation, which was abolished by miR-21 overexpression. Smad7 overexpression rescued the effect of exosomes from TSLP-treated DCs on Th17/Treg differentiation. In conclusion, our article confirms that TSLP induces DCs to deliver miR-21 by secreting exosomes, and thus miR-21 regulates Th17/Treg differentiation by inhibiting Smad7. Thus, this work further reveals the biological role of miR-21 in fungal keratitis.

60 APPLIED LIFE SCIENCES↗