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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Phylogenetic and ecological drivers of the avian lung mycobiome and its potentially pathogenic component

Vertebrate lungs contain diverse microbial communities, but little is known about the drivers of community composition or consequences for health. Microbiome assembly by processes such as dispersal, coevolution, and host-switching can be probed with comparative surveys; however, few studies exist for lung microbiomes, particularly for the fungal component, the mycobiome. Distinguishing among fungal taxa that are generalist or specialist symbionts, potential pathogens, or incidentally inhaled spores is urgent because of potential for emerging diseases. Here, we characterize the avian lung mycobiome and test the relative influences of environment, phylogeny, and functional traits. We used metabarcoding and culturing from 195 lung samples representing 32 bird species across 20 families. We identified 526 fungal taxa as estimated by distinct sequence types (zOTUs) including many opportunistic pathogens. These were predominantly from the phylum Ascomycota (79%) followed by Basidiomycota (16%) and Mucoromycota (5%). Yeast and yeast-like taxa (Malassezia, Filobasidium, Saccharomyces, Meyerozyma, and Aureobasidium) and filamentous fungi (Cladosporium, Alternaria, Neurospora, Fusarium, and Aspergillus) were abundant. Lung mycobiomes were strongly shaped by environmental exposure, and further modulated by host identity, traits, and phylogenetic affinities. Our results implicate migratory bird species as potential vectors for long-distance dispersal of opportunistically pathogenic fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler

Microbial communities drive matter and energy transformations integral to global biogeochemical cycles, yet many taxonomic groups facilitating these processes remain poorly represented in biological sequence databases. Due to this missing information, taxonomic assignment of sequences from environmental genomes remains inaccurate. We present the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software for functionally and taxonomically classifying genes, reactions and pathways from genomes of cultivated and uncultivated microorganisms using reference packages representing coding sequences mediating multiple globally relevant biogeochemical cycles. TreeSAPP uses linear regression of evolutionary distance on taxonomic rank to improve classifications, assigning both closely related and divergent query sequences at the appropriate taxonomic rank. TreeSAPP is able to provide quantitative functional and taxonomic classifications for both assembled and unassembled sequences and files supporting interactive tree of life visualizations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)

Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana—chosen as the model plant system for this reason—as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm the correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Development of modular expression across phylogenetically distinct diazotrophs

Diazotrophic bacteria can reduce atmospheric nitrogen into ammonia enabling bioavailability of the essential element. Many diazotrophs closely associate with plant roots increasing nitrogen availability, acting as plant growth promoters. These associations have the potential to reduce the need for costly synthetic fertilizers if they could be engineered for agricultural applications. However, despite the importance of diazotrophic bacteria, genetic tools are poorly developed in a limited number of species, in turn narrowing the crops and root microbiomes that can be targeted. Here, we report optimized protocols and plasmids to manipulate phylogenetically diverse diazotrophs with the goal of enabling synthetic biology and genetic engineering. Three broad-host-range plasmids can be used across multiple diazotrophs, with the identification of one specific plasmid (containing origin of replication RK2 and a kanamycin resistance marker) showing the highest degree of compatibility across bacteria tested. We then demonstrated modular expression by testing seven promoters and eleven ribosomal binding sites using proxy fluorescent proteins. Finally, we tested four small molecule inducible systems to report expression in three diazotrophs and demonstrated genome editing in Klebsiella michiganensis M5al.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert

The best ideotypes are under mounting pressure due to increased aridity. Understanding the conserved molecular mechanisms that evolve in wild plants adapted to harsh environments is crucial in developing new strategies for agriculture. Yet our knowledge of such mechanisms in wild species is scant. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama and phylogenetically related species that do not live in Atacama (sister species). We analyzed reaction enrichment to understand the commonalities and differences of Atacama plants. To gain insights into the mechanisms that ensure survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and sister species. We found biochemical convergences characterized by reactions enriched in at least 50% of the Atacama species, pointing to potential advantages against drought and nitrogen starvation, for instance. Furthermore, these findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses. Convergent adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Towards mapping biodiversity from above: Can fusing lidar and hyperspectral remote sensing predict taxonomic, functional, and phylogenetic tree diversity in temperate forests?

Abstract Aim Rapid global change is impacting the diversity of tree species and essential ecosystem functions and services of forests. It is therefore critical to understand and predict how the diversity of tree species is spatially distributed within and among forest biomes. Satellite remote sensing platforms have been used for decades to map forest structure and function but are limited in their capacity to monitor change by their relatively coarse spatial resolution and the complexity of scales at which different dimensions of biodiversity are observed in the field. Recently, airborne remote sensing platforms making use of passive high spectral resolution (i.e., hyperspectral) and active lidar data have been operationalized, providing an opportunity to disentangle how biodiversity patterns vary across space and time from field observations to larger scales. Most studies to date have focused on single sites and/or one sensor type; here we ask how multiple sensor types from the National Ecological Observatory Network’s Airborne Observation Platform (NEON AOP) perform across multiple sites in a single biome at the NEON field plot scale (i.e., 40 m × 40 m). Location Eastern USA. Time period 2017–2018. Taxa studied Trees. Methods With a fusion of hyperspectral and lidar data from the NEON AOP, we assess the ability of high resolution remotely sensed metrics to measure biodiversity variation across eastern US temperate forests. We examine how taxonomic, functional, and phylogenetic measures of alpha diversity vary spatially and assess to what degree remotely sensed metrics correlate with in situ biodiversity metrics. Results Models using estimates of forest function, canopy structure, and topographic diversity performed better than models containing each category alone. Our results show that canopy structural diversity, and not just spectral reflectance, is critical to predicting biodiversity. Main conclusions We found that an approach that jointly leverages spectral properties related to leaf and canopy functional traits and forest health, lidar derived estimates of forest structure, fine‐resolution topographic diversity, and careful consideration of biogeographical differences within and among biomes is needed to accurately map biodiversity variation from above.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids

Background The genomic and evolutionary study of allopolyploid organisms involves multiple copies of homeologous chromosomes, making their assembly, annotation, and phylogenetic analysis challenging. Bioinformatics tools and protocols have been developed to study polyploid genomes, but sometimes require the assembly of their genomes, or at least the genes, limiting their use. Results We have developed AlloSHP, a command-line tool for detecting and extracting single homeologous polymorphisms (SHPs) from the subgenomes of allopolyploid species. This tool integrates three main algorithms, WGA, VCF2ALIGNMENT and VCF2SYNTENY, and allows the detection of SHPs for the study of diploid-polyploid complexes with available diploid progenitor genomes, without assembling and annotating the genomes of the allopolyploids under study. AlloSHP has been validated on three diploid-polyploid plant complexes, Brachypodium, Brassica, and Triticum-Aegilops, and a set of synthetic hybrid yeasts and their progenitors of the genus Saccharomyces. The results and congruent phylogenies obtained from the four datasets demonstrate the potential of AlloSHP for the evolutionary analysis of allopolyploids with a wide range of ploidy and genome sizes. Conclusions AlloSHP combines the strategies of simultaneous mapping against multiple reference genomes and syntenic alignment of these genomes to call SHPs, using as input data a single VCF file and the reference genomes of the known or closest extant diploid progenitor species. This novel approach provides a valuable tool for the evolutionary study of allopolyploid species, both at the interspecific and intraspecific levels, allowing the simultaneous analysis of a large number of accessions and avoiding the complex process of assembling polyploid genomes.

Allopolyploids↗
DOE OSTI2024

Insights into the action of phylogenetically diverse microbial expansins on the structure of cellulose microfibrils

Microbial expansins (EXLXs) are non-lytic proteins homologous to plant expansins involved in plant cell wall formation. Due to their non-lytic cell wall loosening properties and potential to disaggregate cellulosic structures, there is considerable interest in exploring the ability of microbial expansins (EXLX) to assist the processing of cellulosic biomass for broader biotechnological applications. Herein, EXLXs with different modular structure and from diverse phylogenetic origin were compared in terms of ability to bind cellulosic, xylosic, and chitinous substrates, to structurally modify cellulosic fibrils, and to boost enzymatic deconstruction of hardwood pulp. Five heterogeneously produced EXLXs (Clavibacter michiganensis; CmiEXLX2, Dickeya aquatica; DaqEXLX1, Xanthomonas sacchari; XsaEXLX1, Nothophytophthora sp.; NspEXLX1 and Phytophthora cactorum; PcaEXLX1) were shown to bind xylan and hardwood pulp at pH 5.5 and CmiEXLX2 (harboring a family-2 carbohydrate-binding module) also bound well to crystalline cellulose. Small-angle X-ray scattering revealed a 20–25% increase in interfibrillar distance between neighboring cellulose microfibrils following treatment with CmiEXLX2, DaqEXLX1, or NspEXLX1. Correspondingly, combining xylanase with CmiEXLX2 and DaqEXLX1 increased product yield from hardwood pulp by ~ 25%, while supplementing the TrAA9A LPMO from Trichoderma reesei with CmiEXLX2, DaqEXLX1, and NspEXLX1 increased total product yield by over 35%. This direct comparison of diverse EXLXs revealed consistent impacts on interfibrillar spacing of cellulose microfibers and performance of carbohydrate-active enzymes predicted to act on fiber surfaces. These findings uncover new possibilities to employ EXLXs in the creation of value-added materials from cellulosic biomass.

09 BIOMASS FUELS↗
DOE OSTI2021

Phylogenetic diversity, trichothecene potential, and pathogenicity within Fusarium sambucinum species complex

The Fusarium sambucinum species complex (FSAMSC) is one of the most taxonomically challenging groups of fusaria, comprising prominent mycotoxigenic plant pathogens and other species with various lifestyles. Among toxins produced by members of the FSAMSC, trichothecenes pose the most significant threat to public health. Herein a global collection of 171 strains, originating from diverse hosts or substrates, were selected to represent FSAMSC diversity. This strain collection was used to assess their species diversity, evaluate their potential to produce trichothecenes, and cause disease on wheat. Maximum likelihood and Bayesian analyses of a combined 3-gene dataset used to infer evolutionary relationships revealed that the 171 strains originally received as 48 species represent 74 genealogically exclusive phylogenetically distinct species distributed among six strongly supported clades: Brachygibbosum, Graminearum, Longipes, Novel, Sambucinum, and Sporotrichioides. Most of the strains produced trichothecenes in vitro but varied in type, indicating that the six clades correspond to type A, type B, or both types of trichothecene-producing lineages. Furthermore, five strains representing two putative novel species within the Sambucinum Clade produced two newly discovered type A trichothecenes, 15-keto NX-2 and 15-keto NX-3. Strains of the two putatively novel species together with members of the Graminearum Clade were aggressive toward wheat when tested for pathogenicity on heads of the susceptible cultivar Apogee. In planta, the Graminearum Clade strains produced nivalenol or deoxynivalenol and the aggressive Sambucinum Clade strains synthesized NX-3 and 15-keto NX-3. Other strains within the Brachygibbosum, Longipes, Novel, Sambucinum, and Sporotrichioides Clades were nonpathogenic or could infect the inoculated floret without spreading within the head. Moreover, most of these strains did not produce any toxin in the inoculated spikelets. These data highlight aggressiveness toward wheat appears to be influenced by the type of toxin produced and that it is not limited to members of the Graminearum Clade.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Plant sulfate transporter protein sequences for phylogenetic analysis

Sulfur is an essential macronutrient that supports plant growth, development, and responses to environmental stress. Sulfate is the predominant inorganic form of sulfur in soils, and its uptake by roots and translocation to shoots are facilitated by the sulfate transporter (SULTR) family of proteins. Although the first plant SULTR gene was identified nearly three decades ago, several subfamily members, particularly those in the expansive and angiosperm-specific SULTR3 group, remain poorly characterized. To support comprehensive phylogenetic and sequence-based analyses, we compiled a curated dataset of 262 SULTR protein sequences from 22 plant species spanning the evolutionary breadth of land plants. This collection includes representatives from two basal lineages, two early-divergent angiosperms, six monocots, and ten dicots. All sequences were extracted from genome assemblies available in Phytozome v13 (Joint Genome Institute) and manually curated, with cross-referencing to additional databases such as NCBI when needed. This dataset provides a valuable resource for reconstructing the evolutionary history of the SULTR family, with particular emphasis on the diversification of SULTR3 transporters in flowering plants. This resource may also support functional annotation, comparative genomics, and structural modeling of sulfate transport proteins.

CBI↗
DOE OSTI2025

Transcriptomics outputs and phylogenetic trees used for pathway discovery of diterpenoid alkaloids in Delphinium and Aconitum

Transcriptome assemblies, open reading frames in nucleotide and peptide sequences, clustered transcriptomes and corresponding amino acid files, and expression matrices in TPM and raw counts for RNA-seq datasets from Delphinium grandiflorum, Aconitum plicatum, Aconitum lycoctonum, Aconitum carmichaelii, Aconitum japonicum, Aconitum kusnezoffii, and Aconitum vilmorinianum. Also included are phylogenetic trees for terpene synthases and cytochromes P450 mined from these assemblies.

biosynthesis↗
DOE OSTI2020

Software classification using phylogenetic techniques

Software, such as malware, may be classified using phylogenetic techniques. An evolutionary history of a representative set of software programs may be reconstructed to generate a reference phylogeny. Dynamic traces of the representative software programs may be obtained. The dynamic traces may include time-ordered sequences of execution commands extracted from running software binaries. Metrics may be developed using the dynamic traces. One or more unknown software programs may then be classified against the reference phylogeny using the metrics developed using the dynamic traces of the representative set of software programs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Phylogenetic occurrence of the phenylpropanoid pathway and lignin biosynthesis in plants

The phenylpropanoid pathway serves as a rich source of metabolites in plants and provides precursors for lignin biosynthesis. Lignin first appeared in tracheophytes and has been hypothesized to have played pivotal roles in land plant colonization. In this review, we summarize recent progress in defining the lignin biosynthetic pathway in lycophytes, monilophytes, gymnosperms, and angiosperms. In particular, we review the key structural genes involved in p-hydroxyphenyl-, guaiacyl- and syringyl-lignin biosynthesis across plant taxa and consider and integrate new insights on major transcription factors, such as NACs and MYBs. We also review insight regarding a new transcriptional regulator, 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, canonically identified as a key enzyme in the shikimate pathway. We use several case studies, including EPSP synthase, to illustrate the evolution processes of gene duplication and neo-functionalization in lignin biosynthesis. This review provides new insights into the genetic engineering of the lignin biosynthetic pathway to overcome biomass recalcitrance in bioenergy crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The core metabolome and root exudation dynamics of three phylogenetically distinct plant species

Abstract Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana , Brachypodium distachyon , and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Phylogenetic diversity of light-dependent phosphorylation of Thr78 in Rubisco activase

Rubisco activase is an ATP-dependent chaperone that facilitates dissociation of inhibitory sugar phosphates from the catalytic sites of Rubisco during photosynthesis. In Arabidopsis, Rubisco activase is negatively regulated by dark-dependent phosphorylation of Thr78. The prevalence of Thr78 in Rubisco activase was investigated across sequences from 91 plant species, finding that 29 (∼32%) species shared a threonine in the same position. Analysis of seven C3 species with an antibody raised against a Thr78 phospho-peptide demonstrated that this position is phosphorylated in multiple genera. However, light-dependent dephosphorylation of Thr78 was observed only in Arabidopsis. Further, phosphorylation of Thr78 could not be detected in any of the four C4 grass species examined. The results suggest that despite conservation of Thr78 in Rubisco activase from a wide range of species, a regulatory role for phosphorylation at this site is more limited. Furthermore, this provides a case study for how variation in post-translational regulation can amplify functional divergence across the phylogeny of plants beyond what is explained by sequence variation in a metabolically important protein.

Arabidopsis↗