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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

Ascomycota, the largest and most well-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts). Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina differ greatly in their genome properties and enabled inference of the direction of evolutionary change. The Saccharomycotina typically have smaller genomes, lower guanine-cytosine contents, lower numbers of genes, and higher rates of molecular sequence evolution compared with Pezizomycotina. These results provide a robust evolutionary framework for understanding the diversity and ecological lifestyles of the largest fungal phylum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes

Giant viruses (GVs) are key players in ecosystem functioning, biogeochemistry, and eukaryotic genome evolution. GV diversity and abundance in aquatic systems can exceed that of prokaryotes, but their diversity and ecology in lakes, especially polar ones, remain poorly understood. We conducted a comprehensive survey and meta-analysis of GV diversity across 20 lakes, spanning polar to temperate regions, combining our extensive lake metagenome database from the Canadian Arctic and subarctic with publicly available datasets. Leveraging a novel GV genome identification tool, we identified 3304 GV metagenome-assembled genomes, revealing lakes as untapped GV reservoirs. Phylogenomic analysis highlighted their dispersion across all Nucleocytoviricota orders. Strong GV population endemism emerged between lakes from similar regions and biomes (Antarctic and Arctic), but a polar/temperate barrier in lacustrine GV populations and differences in their gene content could be observed. Our study establishes a robust genomic reference for future investigations into lacustrine GV ecology in fast changing polar environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species

Pseudomonas putida is a gram-negative bacterial species increasingly utilized in biotechnology due to its robust growth, ability to degrade aromatic compounds, solvent tolerance, and genetic tractability. In this study, we report a comprehensive multi-strain analysis of 164 P. putida strains based on the reconstruction of a pan-putida metabolic network and the formulation of strain-specific genome-scale metabolic models (GEMs). We performed whole-genome sequencing and hybrid assembly for 40 strains, contributing a ~8% increase to the available genomic data for P. putida . Furthermore, high-throughput phenotypic profiling using the Biolog phenotype microarray system for 24 strains on 190 unique carbon sources, along with 15 aromatic compounds not present on Biolog plates, yielded 4,920 unique strain-phenotype measurements. These data were leveraged to curate GEMs for 24 representative strains, including a refined model for strain KT2440, which comprised 1,480 genes and 2,191 metabolites, achieving a prediction accuracy of 91.2% in carbon utilization. Systematic comparison of genomes and GEMs revealed both conserved core pathways and significant allelic and functional divergence across strains, highlighting strain-specific variation in aromatic degradation. While pathways for protocatechuate and phenylacetate degradation were widely conserved, metabolic capabilities for compounds such as ferulate, phenol, and cresols varied markedly, suggesting adaptation to distinct ecological niches. Alleleome analysis of enzymes, such as PcaI and PcaJ, revealed distinct, functionally similar clades, indicating possible convergent evolution or horizontal gene transfer. These results provide computable resources and informative models for selecting P. putida strains with desired traits for biomanufacturing and bioremediation and offer insights into the evolution and phylogeny of the P. putida species.

aromatics utilization↗
DOE OSTI2023

The circular nutrient economy of terrestrial ecosystems and the consequences for rock weathering

Earth’s biosphere is thought to exert a substantial influence on regolith evolution and chemical weathering rates. However, ecosystems are also highly efficient at retaining and recycling nutrients. Thus, when the ecological demand for rock-derived nutrients (e.g., P, Ca, K) exceeds the rates of regolith supply, ecological retention and recycling strategies can minimize nutrient limitations. To evaluate the balance between nutrient recycling and new nutrient input, we combined a plant model that drives growth according to foliar P levels with a weathering model that includes regolith rejuvenation via erosion and export via chemical weathering according to water flow, regolith thickness, mineral dissolution rates, secondary minerals, and nutrient storage in organic and mineral phases. We find that plant growth is strongly dependent on the total regolith nutrient inventory, resulting in a strong correlation between plant productivity and erosion. Increased water export or decreased regolith thickness diminish the total inventory of nutrient corresponding to lower rates of recycling and lower plant growth. In contrast, purported biogenic drivers of weathering, such as enhanced mineral dissolution, only support higher growth rates at high erosion rates. At erosion rates typical of the global land surface, more rapid mineral dissolution combined with enhanced formation of secondary minerals, depletes the inventory of mineral P, resulting in no benefit for plant growth. We also find that the increased chemical weathering export does not scale directly with plant growth. For example, accelerated mineral weathering does increase chemical weathering export but not potential plant growth. Conversely, thicker regolith is associated with a small increase in weathering export, but a large increase in potential plant growth. Collectively, when plant growth is coupled to regolith weathering our calculations suggest that plant productivity is not directly correlated with silicate weathering fluxes, and that biotic drivers of silicate weathering may only be effective at high erosion rates not typical at the Earth’s surface.

58 GEOSCIENCES↗
DOE OSTI2023

Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs

Abstract Giant kelp, Macrocystis pyrifera, exists as distinct morphological variants—or “ecomorphs”—in different populations, yet the mechanism for this variation is uncertain, and environmental drivers for either adaptive or plastic phenotypes have not been identified. The ecomorphs Macrocystis “pyrifera” and M. “integrifolia” are distributed throughout temperate waters of North and South America with almost no geographic overlap and exhibit an incongruous, non-mirrored, distribution across the equator. This study evaluates the degree of genetic divergence between M. “pyrifera” and M. “integrifolia” across 18 populations in Chile and California using whole-genome sequencing and single-nucleotide polymorphism markers. Our results based on a principal component analysis, admixture clustering by genetic similarity, and phylogenetic inference demonstrate that M. “pyrifera” and M. “integrifolia” are genetically distinguishable. Analyses reveal separation by Northern and Southern Hemispheres and between morphs within hemispheres, suggesting that the convergent “integrifolia” morphology arose separately in each hemisphere. This is the first study to use whole-genome sequencing to understand genetic divergence in giant kelp ecomorphs, identifying 83 potential genes under selection and providing novel insights about Macrocystis evolution that were not evident with previous genetic techniques. Future studies are needed to uncover the environmental forces driving local adaptation and presumed convergent evolution of these morphs.

Environmental Sciences & Ecology↗
DOE OSTI2023

Evolution of global snow drought characteristics from 1850 to 2100

Abstract Seasonal snow is an integral part of the global water supply and storage system. Snow droughts impact ecological, agricultural, and urban systems by altering the amount and timing of meltwater delivery. These droughts are characterized by a lack of on-the-ground snow (snow water equivalent, SWE) that can be caused by low total precipitation (dry drought) or low proportion of precipitation falling as snowfall (warm drought), often combined with an early melt. The standardized SWE index (SWEI) ranks the current status of SWE for a given location compared to a baseline condition and identifies the existence, but not the cause, of snow drought. In this work, we use estimates of SWE, temperature, and precipitation from nine coupled model intercomparison project phase 6 (CMIP6) models to quantify the frequency, severity, and type of snow droughts globally for historical and future scenarios. Compared to a historical baseline (1850–1900) total snow drought frequency more than doubles under socio-economic pathway (SSP)2-4.5 and SSP5-8.5; all of the increase in snow drought frequency comes from an increase in warm droughts. The probability distribution of future SWEI in major snowy basins around the world are likely to be centered on more negative values, which corresponds to more severe drought and, with only moderate changes in distribution spread, more frequent drought. CMIP6 simulations pinpoint snow drought as an emerging global threat to water resources and highlight the need to explore higher resolution future models that better capture complex mountain topography, wildland fires, and snow-forest interactions.

CMIP6↗
DOE OSTI2024

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

Summary Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.

Plant Sciences↗
DOE OSTI2026

Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts

Antifungal drug resistance is a major challenge in fungal infection management. Numerous genomic changes are known to contribute to acquired drug resistance in clinical isolates of specific pathogens, but whether they broadly explain natural resistance across entire lineages is unknown. We leveraged genomic, ecological, and phenotypic trait data from naturally sampled strains from nearly all known species in subphylum Saccharomycotina to examine the evolution of resistance to eight antifungal drugs. The phylogenetic distribution of drug resistance varied by drug; fluconazole resistance was widespread, while 5-fluorocytosine resistance was rare, except in Lipomycetales. A random forest algorithm trained on genomic data predicted drug-resistant yeasts with 54–75% accuracy. Fluconazole resistance was consistently predicted with the highest accuracy (75.2%). Furthermore, fluconazole resistance prediction accuracy was similar between models trained on genome-wide variation in the presence and number of InterPro protein annotations across Saccharomycotina (75.2%) and those trained on amino acid sequence alignment data of Erg11, a protein known to be involved in fluconazole resistance (74.3-74.9%). Interestingly, the top Erg11 residues for predicting fluconazole resistance across Saccharomycotina do not overlap with, are not spatially close to, and are less conserved than those previously linked to resistance in clinical isolates of Candida albicans. In silico deep mutational scanning of the C. albicans Erg11 protein reveals that amino acid variants implicated in clinical cases of resistance are almost universally destabilizing while variants in our most informative residues are energetically more neutral, explaining why the latter are much more common than the former in natural populations. Importantly, previous experimental analyses of C. albicans Erg11 have shown that amino acid variation in our most informative residues, despite having never been directly implicated in clinical cases, can directly contribute to resistance. Our results suggest that studies of natural resistance in yeast species never encountered in the clinic will yield a fuller understanding of antifungal drug resistance.

Harrison, Marie-Claire [Vanderbilt Univ., Nashvill↗
DOE OSTI2023

The evolution of anaerobic growth in Saccharomycotina yeasts

Humans rely on the ability of budding yeasts to grow without oxygen in industrial scale fermentations that produce beverages, foods, and biofuels. Oxygen is deeply woven into the energy metabolism and biosynthetic capabilities of budding yeasts. While diverse ecological habitats may provide wide varieties of different carbon and nitrogen sources for yeasts to utilize, there is no direct substitute for molecular oxygen, only a range of availability. Understanding how a small subset of budding yeasts evolved the ability to grow without oxygen could expand the set of useful species in industrial scale fermentations as well as provide insight into the cryptic field of yeast ecology. Furthermore, we still do not yet appreciate the full breadth of species that can growth without oxygen, what genes underlie this adaptation, and how these genes have evolved.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination

Abstract Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in bothSalinibacter ruber, an environmental halophilic organism, andEscherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.

Science & Technology - Other Topics↗
DOE OSTI2024

$\mathrm{COBRA}$ improves the completeness and contiguity of viral genomes assembled from metagenomes

Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Biological response of eelgrass epifauna, Taylor's Sea hare ( Phyllaplysia taylori ) and eelgrass isopod ( Idotea resecata ), to elevated ocean alkalinity

Abstract. Marine carbon dioxide removal (mCDR) approaches are under development to mitigate the effects of climate change by sequestering carbon in stable reservoirs, with the potential co-benefit of local reductions in coastal acidification impacts. One such method is ocean alkalinity enhancement (OAE). A specific OAE method is the generation of aqueous alkalinity via electrochemistry to enhance the alkalinity of the receiving water by the extraction of acid from seawater, thereby avoiding the issues of solid dissolution kinetics and the release of impurities into the ocean from alkaline minerals. While electrochemical acid extraction is a promising method for increasing the carbon dioxide sequestration potential of the ocean, the biological effects of increasing seawater alkalinity and pH within an OAE project site are relatively unknown. This study aims to address this knowledge gap by testing the effects of increased pH and alkalinity, delivered in the form of aqueous NaOH, on two eelgrass epifauna in the US Pacific Northwest, Taylor's sea hare (Phyllaplysia taylori) and eelgrass isopod (Idotea resecata), chosen for their ecological importance as salmon prey and for their role in eelgrass ecosystems. Four-day experiments were conducted in closed bottles to allow measurements of the evolution of carbonate species throughout the experiment, with water refreshed twice daily to maintain elevated pH, across pHNBS (NBS standard scale) treatments ranging from 7.8 to 9.3. Sea hares experienced mortality in all pH treatments, ranging from 37 % mortality at pHNBS 7.8 to 100 % mortality at pHNBS 9.3. Isopods experienced lower mortality rates in all treatment groups, ranging from 13 % at pHNBS 7.8 to 21 % at pHNBS 9.3, which did not significantly increase with higher pH treatments. These experiments represent an extreme of constant exposure to elevated pH and alkalinity, which should be considered in the context of both the natural variation and the dilution of alkalinity experienced by marine communities across an OAE project site. Different invertebrate species will likely have different responses to increased pH and alkalinity, depending on their physiological vulnerabilities. Investigation of the potential vulnerabilities of local marine species will help inform the decision-making process regarding mCDR planning and permitting.

marine carbon dioxide removal↗
DOE OSTI2021

Whole-Genome Comparisons of Ergot Fungi Reveals the Divergence and Evolution of Species within the Genus Claviceps Are the Result of Varying Mechanisms Driving Genome Evolution and Host Range Expansion

The genus Claviceps has been known for centuries as an economically important fungal genus for pharmacology and agricultural research. Only recently have researchers begun to unravel the evolutionary history of the genus, with origins in South America and classification of four distinct sections through ecological, morphological, and metabolic features (Claviceps sects. Citrinae, Paspalorum, Pusillae, and Claviceps). The first three sections are additionally characterized by narrow host range, whereas section Claviceps is considered evolutionarily more successful and adaptable as it has the largest host range and biogeographical distribution. However, the reasons for this success and adaptability remain unclear. Our study elucidates factors influencing adaptability by sequencing and annotating 50 Claviceps genomes, representing 21 species, for a comprehensive comparison of genome architecture and plasticity in relation to host range potential. Our results show the trajectory from specialized genomes (sects. Citrinae and Paspalorum) toward adaptive genomes (sects. Pusillae and Claviceps) through colocalization of transposable elements around predicted effectors and a putative loss of repeat-induced point mutation resulting in unconstrained tandem gene duplication coinciding with increased host range potential and speciation. Alterations of genomic architecture and plasticity can substantially influence and shape the evolutionary trajectory of fungal pathogens and their adaptability. Furthermore, our study provides a large increase in available genomic resources to propel future studies of Claviceps in pharmacology and agricultural research, as well as, research into deeper understanding of the evolution of adaptable plant pathogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An integrative framework reveals widespread gene flow during the early radiation of oaks and relatives in Quercoideae (Fagaceae)

ABSTRACT Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages ofQuercusand relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages ofQuercusand relatives in Quercoideae during their initial radiation, dated to the Early‐Middle Eocene. Ancestral reconstructions including fossils suggest ancestors ofCastanea + Castanopsis,Lithocarpus, and the Old World oak clade probably co‐occurred in North America and Eurasia, while the ancestors ofChrysolepis, Notholithocarpus, and the New World oak clade co‐occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization—perhaps in the form of ancient syngameons like those seen today—has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. Furthermore, these comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Early Oligocene kelp holdfasts and stepwise evolution of the kelp ecosystem in the North Pacific

Kelp forests are highly productive and economically important ecosystems worldwide, especially in the North Pacific Ocean. However, current hypotheses for their evolutionary origins are reliant on a scant fossil record. Here, in this work, we report fossil hapteral kelp holdfasts from western Washington State, USA, indicating that kelp has existed in the northeastern Pacific Ocean since the earliest Oligocene. This is consistent with the proposed North Pacific origin of kelp associated with global cooling around the Eocene–Oligocene transition. These fossils also support the hypotheses that a hapteral holdfast, rather than a discoid holdfast, is the ancestral state in complex kelps and suggest that early kelps likely had a flexible rather than a stiff stipe. Early kelps were possibly grazed upon by mammals like desmostylians, but fossil evidence of the complex ecological interactions known from extant kelp forests is lacking. The fossil record further indicates that the present-day, multi-story kelp forest had developed at latest after the mid-Miocene climate optimum. In summary, the fossils signify a stepwise evolution of the kelp ecosystem in the North Pacific, likely enabled by changes in the ocean-climate system.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource

Abstract Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions

Description of the Earth’s microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, has been a central tenet in the field of ecology because of its implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗