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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions

ABSTRACT Microbial probiotics are intended to improve functions in diverse ecosystems, yet probiotics often fail to establish in a preexisting microbiome. This is a species invasion problem. The relative importance of the two major factors controlling establishment in this context—propagule pressure (inoculation dose and frequency) and biotic interactions (composition of introduced and resident communities)—is unknown. We tested the effect of these factors in driving microbial composition and functioning following 12 microbial community invasions (e.g., introductions of many microbial invaders) in microcosms. Ecosystem functioning over a 30-day postinvasion period was assessed by measuring activity (respiration) and environment modification (dissolved organic carbon abundance). To test the dependence on environmental context, experiments were performed in two resource environments. In both environments, biotic interactions were more important than propagule pressure in driving microbial composition and community function, but the magnitude of effect varied by environment. Successful invaders comprised approximately 8% of the total number of operational taxonomic units (OTUs). Bacteria were better invaders than fungi, with average relative abundances of 7.4% ± 6.8% and 1.5% ± 1.4% of OTUs, respectively. Common bacterial invaders were associated with stress response traits. The most resilient bacterial and fungal families, in other words, those least impacted by invasions, were linked to antimicrobial resistance or production traits. Illuminating the principles that determine community composition and functioning following microbial invasions is key to efficient community engineering. IMPORTANCE With increasing frequency, humans are introducing new microbes into preexisting microbiomes to alter functioning. Example applications include modification of microflora in human guts for better health and those of soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved with a better understanding of microbial invasions. We conducted a microbial community invasion experiment to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Combinatorial Biosynthesis of Sulfated Benzenediol Lactones with a Phenolic Sulfotransferase from Fusarium graminearum PH-1

Total biosynthesis or whole-cell biocatalytic production of sulfated small molecules relies on the discovery and implementation of appropriate sulfotransferase enzymes. Although fungi are prominent biocatalysts and have been used to sulfate drug-like phenolics, no gene encoding a sulfotransferase enzyme has been functionally characterized from these organisms. Here, we identify a phenolic sulfotransferase, FgSULT1, by genome mining from the plant-pathogenic fungus Fusarium graminearum PH-1. We expressed FgSULT1 in a Saccharomyces cerevisiae chassis to modify a broad range of benzenediol lactones and their nonmacrocyclic congeners, together with an anthraquinone, with the resulting unnatural natural product (uNP) sulfates displaying increased solubility. FgSULT1 shares low similarity with known animal and plant sulfotransferases. Instead, it forms a sulfotransferase family with putative bacterial and fungal enzymes for phase II detoxification of xenobiotics and allelochemicals. Among fungi, putative FgSULT1 homologues are encoded in the genomes of Fusarium spp. and a few other genera in nonsyntenic regions, some of which may be related to catabolic sulfur recycling. Computational structure modeling combined with site-directed mutagenesis revealed that FgSULT1 retains the key catalytic residues and the typical fold of characterized animal and plant sulfotransferases. Our work opens the way for the discovery of hitherto unknown fungal sulfotransferases and provides a synthetic biological and enzymatic platform that can be adapted to produce bioactive sulfates, together with sulfate ester standards and probes for masked mycotoxins, precarcinogenic toxins, and xenobiotics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus

Recent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes of all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite their potential, the development of engineering methods for these organisms has been slow due to their complex life cycle, understudied metabolism, and challenging anaerobic culture requirements.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Lipo-Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles That Modulate Bacterial Growth

Lipo-chitooligosaccharides (LCOs) are historically known for their role as microbial-derived signaling molecules that shape plant symbiosis with beneficial rhizobia or mycorrhizal fungi. Recent studies showing that LCOs are widespread across the fungal kingdom have raised questions about the ecological function of these compounds in organisms that do not form symbiotic relationships with plants. To elucidate the ecological function of these compounds, we investigate the metabolomic response of the ubiquitous human pathogen Aspergillus fumigatus to LCOs. Our metabolomics data revealed that exogenous application of various types of LCOs to A. fumigatus resulted in significant shifts in the fungal metabolic profile, with marked changes in the production of specialized metabolites known to mediate ecological interactions. Using network analyses, we identify specific types of LCOs with the most significant effect on the abundance of known metabolites. Extracts of several LCO-induced metabolic profiles significantly impact the growth rates of diverse bacterial species. These findings suggest that LCOs may play an important role in the competitive dynamics of non-plant-symbiotic fungi and bacteria. This study identifies specific metabolomic profiles induced by these ubiquitously produced chemicals and creates a foundation for future studies into the potential roles of LCOs as modulators of interkingdom competition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Expanding the genetic toolkit: adenine and cytosine base editors for gene disruption in Aspergillus niger

Despite revolutionizing fungal genetic engineering, conventional CRISPR/Cas9-mediated knockouts rely on DNA double-strand breaks (DSBs), which can cause unwanted insertions and deletions, chromosomal abnormalities, and cytotoxicity. Base editors such as adenine base editors (ABEs), which convert A‧T to G‧C, and cytosine base editors (CBEs), which convert C‧G to T‧A, offer a safer alternative by enabling predictable, target-specific single-nucleotide changes without introducing DSBs. To overcome the limitations of traditional genome editing in filamentous fungi, we developed efficient base-editing systems in Aspergillus niger . For the first time, we constructed an ABE in A. niger , achieving up to 80% editing efficiency and inducing predictable A-to-G mutations at the intended intron sites, disrupting gene function through mRNA mis-splicing. We also developed a highly efficient CBE system, capable of introducing premature stop codons with 50–100% efficiency. To broaden the editing scope, we implemented a Cas9-NG variant recognizing a relaxed PAM sequence requiring only a single guanine (G), enabling editing at start codons and splice sites. Leveraging this expanded scope, we established gene disruption approaches by targeting start codons via ABE-mediated A-to-G conversions (ATG-to-GTG and ATG-to-ACG) and CBE-mediated C-to-T conversion (ATG-to-ATA). Additionally, our base-editing systems enable multiplex gRNA delivery and marker-free editing of multiple genes. Collectively, the scope-expanding strategies increase the number of genes targetable for disruption by base-editing in A. niger by 26.3% and enable near-complete coverage of 96% of the coding genes. Overall, this work demonstrates the potential of ABE and CBE systems as versatile, efficient, and safer alternatives to DSBs-based gene disruption in filamentous fungi.

Aspergillus↗
DOE OSTI2023

Rapid remodeling of the soil lipidome in response to a drying-rewetting event

Abstract Background Microbiomes contribute to multiple ecosystem services by transforming organic matter in the soil. Extreme shifts in the environment, such as drying-rewetting cycles during drought, can impact the microbial metabolism of organic matter by altering microbial physiology and function. These physiological responses are mediated in part by lipids that are responsible for regulating interactions between cells and the environment. Despite this critical role in regulating the microbial response to stress, little is known about microbial lipids and metabolites in the soil or how they influence phenotypes that are expressed under drying-rewetting cycles. To address this knowledge gap, we conducted a soil incubation experiment to simulate soil drying during a summer drought of an arid grassland, then measured the response of the soil lipidome and metabolome during the first 3 h after wet-up. Results Reduced nutrient access during soil drying incurred a replacement of membrane phospholipids, resulting in a diminished abundance of multiple phosphorus-rich membrane lipids. The hot and dry conditions increased the prevalence of sphingolipids and lipids containing long-chain polyunsaturated fatty acids, both of which are associated with heat and osmotic stress-mitigating properties in fungi. This novel finding suggests that lipids commonly present in eukaryotes such as fungi may play a significant role in supporting community resilience displayed by arid land soil microbiomes during drought. As early as 10 min after rewetting dry soil, distinct changes were observed in several lipids that had bacterial signatures including a rapid increase in the abundance of glycerophospholipids with saturated and short fatty acid chains, prototypical of bacterial membrane lipids. Polar metabolites including disaccharides, nucleic acids, organic acids, inositols, and amino acids also increased in abundance upon rewetting. This rapid metabolic reactivation and growth after rewetting coincided with an increase in the relative abundance of firmicutes, suggesting that members of this phylum were positively impacted by rewetting. Conclusions Our study revealed specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. The drought-induced nutrient limitation was reflected in the lipidome and polar metabolome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long-chain polyunsaturated fatty acids in dry soil suggest that lipids likely play an important role in the drought tolerance of microbial taxa capable of synthesizing these lipids. An increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest a metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

IMA genome-F18

Sequencing fungal genomes has now become very common and the list of genomes in this manuscript reflects this. Particularly relevant is that the first announcement is a re-identification of Penicillium genomes available on NCBI. The fact that more than 100 of these genomes have been deposited without the correct species names speak volumes to the fact that we must continue training fungal taxonomists and the importance of the International Mycological Association (after which this journal is named). When we started the genome series in 2013, one of the essential aspects was the need to have a phylogenetic tree as part of the manuscript. This came about as the result of a discussion with colleagues in NCBI who were trying to deal with the very many incorrectly identified bacterial genomes (at the time) which had been submitted to NCBI. We are now in the same position with fungal genomes. Sequencing a fungal genome is all too easy but providing a correct species name and ensuring that the fungus has in fact been correctly identified seems to be more difficult. We know that there are thousands of fungi which have not yet been described. The availability of sequence data has made identification of fungi easier but also serves to highlight the need to have a fungal taxonomist in the project to make sure that mistakes are not made.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism

Ploidy is an evolutionarily labile trait, and its variation across the tree of life has profound impacts on evolutionary trajectories and life histories. The immediate consequences and molecular causes of ploidy variation on organismal fitness are frequently less clear, although extreme mating type skews in some fungi hint at links between cell type and adaptive traits. Here, we report an unusual recurrent ploidy reduction in replicate populations of the budding yeast Saccharomyces eubayanus experimentally evolved for improvement of a key metabolic trait, the ability to use maltose as a carbon source. We find that haploids have a substantial, but conditional, fitness advantage in the absence of other genetic variation. Using engineered genotypes that decouple the effects of ploidy and cell type, we show that increased fitness is primarily due to the distinct transcriptional program deployed by haploid-like cell types, with a significant but smaller contribution from absolute ploidy. The link between cell-type specification and the carbon metabolism adaptation can be traced to the noncanonical regulation of a maltose transporter by a haploid-specific gene. This study provides novel mechanistic insight into the molecular basis of an environment–cell type fitness interaction and illustrates how selection on traits unexpectedly linked to ploidy states or cell types can drive karyotypic evolution in fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A glycan receptor kinase facilitates intracellular accommodation of arbuscular mycorrhiza and symbiotic rhizobia in the legume Lotus japonicus

Receptors that distinguish the multitude of microbes surrounding plants in the environment enable dynamic responses to the biotic and abiotic conditions encountered. In this study, we identify and characterise a glycan receptor kinase, EPR3a, closely related to the exopolysaccharide receptor EPR3. Epr3a is up-regulated in roots colonised by arbuscular mycorrhizal (AM) fungi and is able to bind glucans with a branching pattern characteristic of surface-exposed fungal glucans. Expression studies with cellular resolution show localised activation of the Epr3a promoter in cortical root cells containing arbuscules. Fungal infection and intracellular arbuscule formation are reduced in epr3a mutants. In vitro , the EPR3a ectodomain binds cell wall glucans in affinity gel electrophoresis assays. In microscale thermophoresis (MST) assays, rhizobial exopolysaccharide binding is detected with affinities comparable to those observed for EPR3, and both EPR3a and EPR3 bind a well-defined β-1,3/β-1,6 decasaccharide derived from exopolysaccharides of endophytic and pathogenic fungi. Both EPR3a and EPR3 function in the intracellular accommodation of microbes. However, contrasting expression patterns and divergent ligand affinities result in distinct functions in AM colonisation and rhizobial infection in Lotus japonicus . The presence of Epr3a and Epr3 genes in both eudicot and monocot plant genomes suggest a conserved function of these receptor kinases in glycan perception.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Monitoring the impact of confinement on hyphal penetration and fungal behavior

Through their expansive mycelium network, soil fungi alter the physical arrangement and chemical composition of their local environment. This can significantly impact bacterial distribution and nutrient transport and can play a dramatic role in shaping the rhizosphere around a developing plant. However, direct observation and quantitation of such behaviors is extremely difficult due to the opacity and complex porosity of the soil microenvironment. In this study, we demonstrate the development and use of an engineered microhabitat to visualize fungal growth in response to varied levels of confinement. Microfluidics were fabricated using photolithography and conventional soft lithography, assembled onto glass slides, and prepared to accommodate fungal cultures. Selected fungal strains across three phyla (Ascomycota: Morchella sextalata , Fusarium falciforme ; Mucoromycota: Linnemannia elongata , Podila minutissima , Benniella ; Basidiomycota: Laccaria bicolor , and Serendipita sp.) were cultured within microhabitats and imaged using time-lapse microscopy to visualize development at the mycelial level. Fungal hyphae of each strain were imaged as they penetrated through microchannels with well-defined pore dimensions. The hyphal penetration rates through the microchannels were quantified via image analysis. Other behaviors, including differences in the degree of branching, peer movement, and tip strength were also recorded for each strain. Our results provide a repeatable and easy-to-use approach for culturing fungi within a microfluidics platform and for visualizing the impact of confinement on hyphal growth and other fungal behaviors pertinent to their remodeling of the underground environment.

Guo, Yi-Syuan (ORCID:0000000340142225)↗
DOE OSTI2021

A trait-based framework for linking microbial communities with carbon transformations under precipitation change

Droughts are common throughout the world. As the climate changes, droughts may become more frequent and intense. Still, scientists are uncertain about how drought will affect the natural world, particularly the bacteria, fungi, and other microbes that live in soils. These tiny life forms are crucial because they control the Earth’s flows of carbon and essential nutrients. Researchers at the University of California, Irvine, and Lawrence Berkeley National Laboratory teamed up to study how the microbiome, or collection of bacteria and fungi in the soil, deals with drought. Since 2007, the researchers have used shelters with retractable roofs to prevent nearly half of normal rainfall from reaching grass and shrub ecosystems, and their soil microbiomes, in Southern California. The study team discovered that microbes have some clever tricks up their sleeve for surviving drought. When growing on dead grass as a food source, microbes ramp up production of specialized chemicals called osmolytes that keep their cells from drying out. But microbes growing on dead shrubs face another problem. Unlike grass, shrub leaves are a lousy food source. To digest and consume shrub leaves, microbes have to exude more enzymes, which act like biochemical chef knives that chop complex leaf molecules into bite-sized pieces. Carbon is the coin of the microbial realm, earned via enzyme action or slurping up dead plant juices. Microbes growing under normal conditions on tasty dead grass have it easy: they can spend most of their carbon currency on growth. With drought, life gets harder as microbes need to pay up for osmolytes and ramp down their growth. It gets worse with shrub leaves because microbes have to multi-task among growth, enzyme secretion, and osmolyte production. When drought hits, microbes on shrub leaves forgo the osmolytes, probably because losing the carbon revenue from enzyme investment would be a deal-breaker for survival. The next question tackled by the researchers asked how the genes controlling microbial lifestyles sort out across the tree of life. Most microbiologists thought these lifestyles would correspond to rather large branches on the tree. But the study team found that in fact, very closely related microbes differ in important and interesting ways. For example, bacteria that have nearly identical housekeeping genes respond distinctively to warming, rainfall, and plant chemistry. As a result, soil microbiomes are much richer in diversity than originally thought. And studying microbial diversity in much greater detail could open up many more possibilities for how microbial life deals with changing environmental conditions. Trying to understand microbial life without the fine details of genetic diversity is like trying to stream Netflix on a dial-up connection. By looking across the landscape, the researchers revealed that microbial diversity is absolutely critical for maintaining the planet’s flows of carbon and nutrients. The study team designed a new technology—microbial cages—for transplanting intact microbiomes. With the cages, the researchers could move microbiomes to novel environments and compare their ability to cycle carbon and nutrients. In some cases, performance tailed off when microbiomes found themselves in a new environment, but in other cases, performance rivaled or even exceeded that of the resident microbiome. And even the low performers eventually caught up to the native microbiomes if given sufficient time. These findings mean that microbiomes—at least in Southern California—may be resilient to climate shifts due to a high diversity of microbial lifestyles. Coping with heat and drought may literally be in their DNA. The last piece of the research puzzle, and a “Holy Grail” for microbial ecologists, is to forecast the behavior of diverse microbiomes. To meet this challenge, the study team developed new theory and computer models. For the first time, these models account for hundreds of different microbes and how their intricate lifestyles cope with drought. The models are starting to connect the tiniest microbes with the global cycles that sustain Earth’s farms, fields, and forests. With that connection, it will be easier for society to plan for a world with more droughts and other climate disruptions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Synthetic Microbial Consortium for Biological Breakdown and Conversion of Lignin

The plant polymer lignin is the most abundant renewable source of aromatics on the planet and conversion of it to valuable fuels and chemicals is critical to the economic viability of a lignocellulosic biofuels industry and to meeting the DOE’s 2022 goal of $\$2.50$/gallon mean biofuel selling price. Presently, there is no efficient way of converting lignin into valuable commodities. Current biological approaches require mixtures of expensive ligninolytic enzymes and engineered microbes. This project was aimed at circumventing these problems by discovering commensal relationships among fungi and bacteria involved in biological lignin utilization and using this knowledge to engineer microbial communities capable of converting lignin into renewable fuels and chemicals. Essentially, we aimed to learn from, mimic and improve on nature. We discovered fungi that synergistically work together to degrade lignin, engineered fungal systems to increase expression of the required enzymes and engineered organisms to produce products such as biodegradable plastics precursors.

09 BIOMASS FUELS↗
DOE OSTI2024

Live-Cell Quantum Dot-Based Tracking of Plant & Microbial Extracellular Vesicles

All cellular organisms examined to date release various types of small vesicles called extracellular vesicles (EVs). They were originally thought to be unimportant, but research into EVs as carriers of key messages for communication within large, multicellular organisms or between interacting organisms has gained interest in many different scientific areas of study. Recently, it was discovered that both plants and their pathogenic fungi generate EVs and they are important vehicles for sending plant signals to thwart invasion by fungal pathogens, and in response, fungi use EVs to help evade plant defenses. This project aimed to develop new ways to visualize EVs and their potential nucleic acid cargo isolated from the crop plant, sorghum. We adapted a click chemistry-based method for making quantum dot-based RNA sensors, which will be a useful tool for others studying small RNAs. These sensors were not used detect RNA in sorghum EVs because unlike EVs from Arabidopsis, sorghum EVs were not enriched for specific small RNAs. This interesting difference shifted the project in an exciting direction, which focused on comparing EV proteomes. Our study discovered that greater than 60% of Arabidopsis EV proteins were also found in the sorghum EV proteome, revealing a partial conservation between a eudicot and monocot plant. These studies have raised new, fundamental questions on the conserved function of EVs in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

CRADA Number NFE-24-10495 with Algaeo, LLC (CRADA Final Report)

This study investigated the potential for a synthetic consortium of mutualistic terrestrial microbes— comprising the fungi Laccaria bicolor and Serendipita indica alongside bacterial Pseudomonas strains—to influence the growth and productivity of the freshwater microalgae Chlorella vulgaris. The project aimed to determine if microbial complexes engineered to enhance terrestrial plant growth could provide similar growth-promoting benefits or pathogen resistance within an aquatic algal system. Using a quantitative experimental design, C. vulgaris was co-cultured with the microbial mix under controlled laboratory conditions, with growth rates, biomass density, and metabolic activity monitored over a standard cultivation period. The results demonstrated no significant symbiotic relationship or growth enhancement between these terrestrial microbes and the microalgae, as the C. vulgaris maintained independent growth trajectories unaffected by the fungal or bacterial inoculants. We conclude that the specialized mutualisms of these fungi and bacteria are likely niche-specific to vascular plants and do not readily translate to the phycosphere of C. vulgaris. These findings are valuable to synthetic biologists and bioenergy researchers, as they define the functional boundaries of inter-kingdom microbial engineering and underscore the necessity of selecting niche-compatible species when designing consortia for industrial algal cultivation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Interrelationships among methods of estimating microbial biomass across multiple soil orders and biomes: Supporting data

This dataset contains environmental and soil measurements from 18 different locations across the globe including the SPRUCE experiment site and multiple sampling depths, with 17 of these locations having samples processed between 2012-2013 and one location (SPRUCE) collected in 2021 and processed in 2022. Environmental measurements include: mean annual temperature, mean annual precipitation, and 30-day presampling temperature. Soil physicochemical measurements include: particle size analysis (PSA), pH, gravimetric moisture content (GMC), bulk soil carbon (C) and nitrogen (N), total organic C and N, C:N ratio, and dissolved organic carbon (DOC). Soil biological measurements include: microbial biomass carbon (MBC) measured through chloroform fumigation extraction (CFE), gene copy numbers (GCN) of bacteria, fungi, and archaea measured through quantitative polymerase chain reaction (qPCR), DNA yield measured through Nanodrop spectrophotometry, and phospholipid fatty acids (PLFA) of bacteria and fungi measured through PLFA analysis. This data set contains one file in comma separate (*.csv) format.

archaea gene copy number↗
DOE OSTI2021

KS4A-Omics1.0_FspDS682

Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils, because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hotspots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood. Here, we addressed this knowledge gap by directly visualizing nutrient acquisition and transport through fungal hyphae in a mineral doped soil micromodel using a multimodal imaging approach. Here, we observed how a representative of common saprotrophic soil fungi, Fusarium sp. DS 682, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces (~12 μm) in the presence of minerals.This study establishes the significance of fungal biology and nutrient translocation mechanisms in maintaining fungal growth under water and nutrient limitations in a soil-like microenvironment, using a high-throughput multi-omic analysis approach. Data package KS4A-Omics.1.0_FspDS682 (Publication: Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization) contents reported here are the first version (1.0) and contain pre- and post-processed data using high throughput data capture technologies for multi-omic analysis and integration, this data package contains raw and post-processed experimental data for X-Ray Absorption Near Edge Structure Spectroscopy (XANES/XRF), Optical Microscopy, Proteomics, Scanning Electron Microscope (SEM), Time-of-Flight Secondary Ion Mass Spectroscopy (ToF-SIMS), X-Ray Diffraction Spectroscopy (XRD) files, and X- Ray Photoelectron Spectroscopy (XPS) using EMSL capabilities. This data package DOI contains a comprehensive collection of high-throughput multi-omics data and process metadata catalog. Support files include additional data download contents “Read Me” with dataset descriptor information and data source method application ontologies (see data dictionary section). Reported data download content is structured for compliance with reported guidelines provided by community standard initiatives and publisher stakeholder policies supporting FAIR data principles.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Integrative Modeling and Analysis of Fungal Central Carbon Metabolism

Over a thousand fungal genomes have been sequenced, yet manually curated genome-scale metabolic models (GEMs) are available for only a limited number of species. Moreover, these models have often been developed independently, leading to inconsistencies in namespaces, compartment definitions, and pathway representations that hinder comparative analysis, the systematic reuse of prior curation efforts, and the integration of consolidated metabolic knowledge. Here, we present the Consolidated Fungal Core Metabolism Model (CFCMM), constructed by integrating thirteen published fungal models spanning Ascomycota, Mucoromycota, and both Crabtree-positive and Crabtree-negative yeasts. We harmonized metabolites and reactions into a non-redundant shared ModelSEED ontological space, standardized compartmentalization, and refined gene–protein–reaction (GPR) rules. Using pathway-level visualization and systematic gap detection, we further improved the integrated network through literature-guided curation to correct stoichiometry, stereospecificity, and pathway architecture. Orthologous protein family reconstruction and functional annotation workflows were used to validate and inform GPR associations, with particular emphasis on ambiguous enzyme superfamilies and membrane-associated components. Using the resulting CFCMM, we built high-quality central carbon core models for each fungus and performed flux balance analysis to quantify ATP-yield variation under aerobic and anaerobic conditions, explicitly evaluating scenarios driven by differences in electron transport chain (ETC) composition. Simulations reproduced the expected fermentative yield of approximately 2 mmol ATP per mmol glucose under anaerobic conditions and separated the thirteen fungi into two bioenergetic groups under aerobic respiration based on Complex I status, with predicted yields of approximately 30 versus 22 mmol ATP per mmol glucose. Forcing flux through the alternative oxidase bypass further reduced ATP yields to approximately 12 and 4 mmol ATP per mmol glucose in Complex I-containing and Complex I-lacking fungi, respectively. Collectively, this work provides a manually curated, ModelSEED-consistent, and extensible fungal core metabolic template, deployed in DOE KBase as a resource for automated reconstruction of central carbon core models from any sequenced fungal genome. In addition, the CFCMM provides modular components for developing GEMs with more accurate energy predictions and enables robust comparative analyses of fungal bioenergetics and core metabolic diversity

59 BASIC BIOLOGICAL SCIENCES↗