Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “fungi”

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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Comparative Penicillium spp. Transcriptomics: Conserved Pathways and Processes Revealed in Ungerminated Conidia and during Postharvest Apple Fruit Decay

Blue mold, caused by Penicillium spp., is an impactful postharvest disease resulting in significant economic losses due to reduced pome fruit quality and mycotoxin contamination. Using two Penicillium species with different levels of aggressiveness, transcriptomics were implemented in order to identify genes expressed during apple fruit decay and loci expressed in ungerminated conidia. Total RNA was isolated from ungerminated conidia and decayed apple fruit infected with P. expansum R19 or P. polonicum RS1. There were 2442 differentially expressed genes (DEGs) between the R19 and RS1 in apple. Comparisons within species between apple and conidia revealed 4404 DEGs for R19 and 2935 for RS1, respectively. Gene ontology (GO) analysis revealed differential regulation in fungal transport and metabolism genes during decay, suggesting a flux in nutrient acquisition and detoxification strategies. In R19, the oxidoreductase GO category comprised 20% of all DEG groups in apple verses conidia. Ungerminated conidia from both species showed DEGs encoding the glyoxylate shunt and beta-oxidation, specifying the earliest metabolic requirements for germination. This is the first study to identify pre-loaded transcripts in conidia from blue mold fungi, reveal unique genes between species expressed during apple decay, and show the expression dynamics of known fungal virulence factors. These findings will enable development of targeted approaches for blue mold abatement strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Taxonomy and Identification of Principal Foliar Nematode Species ( Aphelenchoides and Litylenchus )

Nematodes are Earth’s most numerous multicellular animals and include species that feed on bacteria, fungi, plants, insects, and animals. Foliar nematodes are mostly pathogens of ornamental crops in greenhouses, nurseries, forest trees, and field crops. Nematode identification has traditionally relied on morphological and anatomical characters using light microscopy and, in some cases, scanning electron microscopy (SEM). This review focuses on morphometrical and brief molecular details and key characteristics of some of the most widely distributed and economically important foliar nematodes that can aid in their identification. Aphelenchoides genus includes some of the most widely distributed nematodes that can cause crop damages and losses to agricultural, horticultural, and forestry crops. Morphological details of the most common species of Aphelenchoides (A. besseyi, A. bicaudatus, A. fragariae, A. ritzemabosi) are given with brief molecular details, including distribution, identification, conclusion, and future directions, as well as an updated list of the nominal species with its synonyms. Litylenchus is a relatively new genus described in 2011 and includes two species and one subspecies. Species included in the Litylenchus are important emerging foliar pathogens parasitizing trees and bushes, especially beech trees in the United States of America. Brief morphological details of all Litylenchus species are provided.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Characterisation and comparative analysis of mitochondrial genomes of false, yellow, black and blushing morels provide insights on their structure and evolution

Morchella species have considerable significance in terrestrial ecosystems, exhibiting a range of ecological lifestyles along the saprotrophism-to-symbiosis continuum. However, the mitochondrial genomes of these ascomycetous fungi have not been thoroughly studied, thereby impeding a comprehensive understanding of their genetic makeup and ecological role. In this study, we analysed the mitogenomes of 30 Morchellaceae species, including yellow, black, blushing and false morels. These mitogenomes are either circular or linear DNA molecules with lengths ranging from 217 to 565 kbp and GC content ranging from 38% to 48%. Fifteen core protein-coding genes, 28–37 tRNA genes and 3–8 rRNA genes were identified in these Morchellaceae mitogenomes. The gene order demonstrated a high level of conservation, with the cox1 gene consistently positioned adjacent to the rnS gene and cob gene flanked by apt genes. Some exceptions were observed, such as the rearrangement of atp6 and rps3 in Morchella importuna and the reversed order of atp6 and atp8 in certain morel mitogenomes. However, the arrangement of the tRNA genes remains conserved. We additionally investigated the distribution and phylogeny of homing endonuclease genes (HEGs) of the LAGLIDADG (LAGs) and GIY-YIG (GIYs) families. A total of 925 LAG and GIY sequences were detected, with individual species containing 19–48HEGs. These HEGs were primarily located in the cox1, cob, cox2 and nad5 introns and their presence and distribution displayed significant diversity amongst morel species. These elements significantly contribute to shaping their mitogenome diversity. Overall, this study provides novel insights into the phylogeny and evolution of the Morchellaceae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Modeling microbial carbon fluxes and stocks in global soils from 1901 to 2016

Abstract. Soil microbes play a crucial role in the carbon (C) cycle; however, they have been overlooked in predicting the terrestrial C cycle. We applied a microbial-explicit Earth system model – the Community Land Model-Microbe (CLM-Microbe) – to investigate the dynamics of soil microbes during 1901 to 2016. The CLM-Microbe model was able to reproduce the variations of gross (GPP) and net (NPP) primary productivity, heterotrophic (HR) and soil (SR) respiration, microbial (MBC) biomass C in fungi (FBC) and bacteria (BBC) in the top 30 cm and 1 m, and dissolved (DOC) and soil organic C (SOC) in the top 30 cm and 1 m during 1901–2016. During the study period, simulated C variables increased by approximately 12 PgC yr−1 for HR, 25 PgC yr−1 for SR, 1.0 PgC for FBC and 0.4 PgC for BBC in 0–30 cm, and 1.2 PgC for FBC and 0.7 PgC for BBC in 0–1 m. Increases in microbial C fluxes and pools were widely found, particularly at high latitudes and in equatorial regions, but we also observed their decreases in some grids. Overall, the area-weighted averages of HR, SR, FBC, and BBC in the top 1 m were significantly correlated with those of soil moisture and soil temperature in the top 1 m. These results suggested that microbial C fluxes and pools were jointly governed by vegetation C input and soil temperature and moisture. Our simulations revealed the spatial and temporal patterns of microbial C fluxes and pools in response to environmental change, laying the foundation for an improved understanding of soil microbial roles in the global terrestrial C cycle.

He, Liyuan↗
DOE OSTI2022

Supporting hierarchical soil biogeochemical modeling: version 2 of the Biogeochemical Transport and Reaction model (BeTR-v2)

Abstract. Reliable soil biogeochemical modeling is a prerequisite for credible projections of climate change and associated ecosystem feedbacks. This recognition has called for frameworks that can support flexible and efficient development and application of new or alternative soil biogeochemical modules in Earth system models (ESMs). The the Biogeochemical Transport and Reaction model version 1 (BeTR-v1) code (i.e., CLM4-BeTR) is one such framework designed to accelerate the development and integration of new soil biogeochemistry formulations into ESMs and to analyze structural uncertainty in ESM simulations. With a generic reactive transport capability, BeTR-v1 can represent multiphase (e.g., gaseous, aqueous, and solid), multi-tracer (e.g., nitrate and organic carbon), and multi-organism (e.g., plants, bacteria, and fungi) dynamics. Here, we describe the new version, Biogeochemical Transport and Reaction model version 2 (BeTR-v2), which adopts more robust numerical solvers for multiphase diffusion and advection and coupling between biogeochemical reactions and improves code modularization over BeTR-v1. BeTR-v2 better supports different mathematical formulations in a hierarchical manner by allowing the resultant model be run for a single topsoil layer or a vertically resolved soil column, and it allows the model to be fully coupled with the land component of the Energy Exascale Earth System Model (E3SM). We demonstrate the capability of BeTR-v2 with benchmark cases and example soil biogeochemical (BGC) implementations. By taking advantage of BeTR-v2's generic structure integrated in E3SM, we then found that calibration could not resolve biases introduced by different numerical coupling strategies of plant–soil biogeochemistry. These results highlight the importance of numerically robust implementation of soil biogeochemistry and coupling with hydrology, thermal dynamics, and plants – capabilities that the open-source BeTR-v2 provides. We contend that Earth system models should strive to minimize this uncertainty by applying better numerical solvers.

58 GEOSCIENCES↗
DOE OSTI2020

Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil’s opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Genome assembly UWOPS 85-398.1-1

The yeast genus Torulaspora (subphylum Saccharomycotina, family Saccharomycetaceae) is mostly known from its type species T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains ten species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of Torulaspora strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of Torulaspora. We also sketch a genotype-phenotype map for the genus and show how key genes have evolved in concert with the physiological traits they control. This dramatic increase in the number of species in the genus Torulaspora highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomics approaches can foster the assessment of species circumscriptions in fungi, especially when classical approaches relying on DNA barcode regions give inconclusive results.

Sampaio, Jose P. [UCIBIO, Departamento de Ciências↗
DOE OSTI2025

Genome assembly UFMG-CM Y6992

The yeast genus Torulaspora (subphylum Saccharomycotina, family Saccharomycetaceae) is mostly known from its type species T. delbrueckii, a frequent colonizer of wine and sourdough bread fermentations. The genus currently contains ten species that are typically found in various natural terrestrial environments in temperate and tropical climates. Here we employ taxogenomic analyses to investigate a large collection of Torulaspora strains obtained in multiple surveys we carried out in Asia, Australasia, North America, South America, and Europe, and to which we added several strains maintained in culture collections. Our analyses detected twelve novel species that are formally described here, thereby more than doubling the species diversity of Torulaspora. We also sketch a genotype-phenotype map for the genus and show how key genes have evolved in concert with the physiological traits they control. This dramatic increase in the number of species in the genus Torulaspora highlights how limited the current inventory of fungal taxa is. It also shows how integrated taxogenomics approaches can foster the assessment of species circumscriptions in fungi, especially when classical approaches relying on DNA barcode regions give inconclusive results.

Sampaio, Jose P. [UCIBIO, Departamento de Ciências↗
NASA NTRS1972

Analysis of fungal type isolates taken from a 90-day manned test of an advanced regenerative life support system

Fungal-like cultures isolated before, during, and after the 90-day test from samples of space station simulator (SSS) atmosphere, surfaces, subsystem componets, and crew dermal sites were identified to genus. Out of the original 525 isolates, approximately 80% were classified as bacteria. Laboratory methods (culture media, moisturization, and incubation temperatures) favored the recovery of medically significant bacteria rather than fungi. Therefore, fungal isolates were mostly, nonfastidious types which are ubiquitous in soil and air and commonly contaminate laboratory cultures of pathogens. Predominant isolates were species of Aspergillus, Penicillium, Pullularia, Rhodotorula, and various yeasts. No instances of fungal proliferation were observed; test data reflect the survival of environmental types indigenous to the SSS pretests.

Sofios, M.↗
NASA NTRS1971

Microbial survival in deep space environment.

Review of the knowledge available on the extent to which microorganisms (mainly microbial spores, vegetative cells, and fungi) are capable of surviving the environment of deep space, based on recent simulation experiments of deep space. A description of the experimental procedures used is followed by a discussion of deep space ecology, the behavior of microorganisms in ultrahigh vacuum, and factors influencing microbial survival. It is concluded that, so far, simulation experiments have proved far less lethal to microorganisms than to other forms of life. There are, however, wide gaps in the knowledge available, and no accurate predictions can as yet be made on the degree of lethality that might be incurred by a microbial population on a given mission. Therefore, sterilization of spacecraft surfaces is deemed necessary if induced panspermia (i.e., interplanetary life propagation) is to be avoided.

Silverman, G. J.↗
NASA NTRS1972

Spacecraft sterilization.

Spacecraft sterilization is a vital factor in projects for the successful biological exploration of other planets. The microorganisms of major concern are the fungi and bacteria. Sterilization procedures are oriented toward the destruction of bacterial spores. Gaseous sterilants are examined, giving attention to formaldehyde, beta-propiolactone, ethylene oxide, and the chemistry of the bactericidal action of sterilants. Radiation has been seriously considered as another method for spacecraft sterilization. Dry heat sterilization is discussed together with the effects of ethylene oxide decontamination and dry heat sterilization on materials.

Kalfayan, S. H.↗
NASA NTRS1973

Crew microbiology (DTO 71-19)

States of microbial imbalance as a result of human altitude chamber confinement occurred, for the most part, only in those genera and species of bacteria, yeast, and fungi which are classified as transients and are not part of the true indigenous flora of the crewmembers. Inasmuch as no crew illness events occurred and only subtle changes in the indigenous flora were noted, it appears that confinement of 56-days in a Skylab simulated environment does not mediate toward shifts in bacterial populations which have obvious clinical significance.

Wooley, B. C.↗
NASA NTRS1973

Introduction

Probable climatic extremes of terrestrial environment data specifically applicable for NASA space vehicles and associated equipment development are considered. Design guideline values are established for the following environmental parameters: (1) Thermal (temperature and solar radiation); (2) humidity; (3) precipitation; (4) winds; (5) pressure; (6) density; (7) electricity (atmospheric); (8) corrosion (atmospheric); (9) sand and dust; (10) fungi and bacteria; (11) atmospheric oxidants; (12) composition of the atmosphere; and (13) inflight thermodynamic properties.

Daniels, G. E.↗
NASA NTRS1974

Microbiological and experimental-histological investigations of lunar samples returned by the Lunar 16 automatic station

Lunar surface material was studied for its content of viable microorganisms (aerobic and anaerobic, fungi, and viruses); the effect of the lunar surface material on the growth of microorganisms and its interaction with somatic cells of mammals was also observed. No viable microorganisms were detected; the samples exhibited neither stimulant or inhibitory action on the growth of microorganisms, and also showed no cytopathogenic action on tissue cultures. A suspension of lunar surface material particles was not toxic when parenterally administered to certain laboratory animals. The particles were subjected to intense phagocytosis by connective tissue cells in vivo and in vitro.

Kaulen, D. R.↗