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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Expanded diversity of novel hemoplasmas in rare and undersampled Neotropical bats

Hemotropic mycoplasmas are emerging as a model system for studying bacterial pathogens in bats, but taxonomic coverage of sampled host species remains biased. We leveraged a long-term field study in Belize to uncover novel hemoplasma diversity in bats by analyzing 80 samples from 19 species, most of which are infrequently encountered. PCR targeting the partial 16S rRNA gene found 41% of bats positive for hemoplasmas. Phylogenetic analyses found two novel host shifts of hemoplasmas, four entirely new hemoplasma genotypes, and the first hemoplasma detections in four bat species. One of these novel hemoplasmas (from Neoeptesicus furinalis) shared 97.6% identity in the partial 16S rRNA gene to a human hemoplasma (Candidatus Mycoplasma haemohominis). Additional analysis of the partial 23S rRNA gene allowed us to also designate two novel hemoplasma species, in Myotis elegans and Phyllostomus discolor, with the proposed names Candidatus Mycoplasma haematomyotis sp. nov. and Candidatus Mycoplasma haematophyllostomi sp. nov., respectively. Our analyses show that additional hemoplasma diversity in bats can be uncovered by targeting rare or undersampled host species.

16S rRNA gene↗
DOE OSTI2022

Diversity in the soil virosphere: to infinity and beyond?

Viruses are key members of Earth’s microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome and metatranscriptome analyses that offer unprecedented windows into the soil virosphere. Given the emerging picture of high soil viral activity, diversity, and dynamics over short spatiotemporal scales, we then outline key eco-evolutionary processes that we hypothesize are the major diversity drivers for soil viruses. We argue that a community effort is needed to establish a 'global soil virosphere atlas' that can be used to address the roles of viruses in soil microbiomes and terrestrial biogeochemical cycles across spatiotemporal scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ligand Control of Structural Diversity in Luminescent Hybrid Copper(I) Iodides

Copper(I) iodide hybrids are of interest for next-generation lighting technologies because of their efficient luminescence in the absence of rare-earth elements. Here, we report 10 structurally diverse hybrid copper(I) iodides that emit in the green–red region with quantum yields reaching 67%. The compounds display a diversity of structures including ones with one-dimensional (1D) Cu–1 chains, Cu 2 I 2 rhomboid dimers, and structures with two different arrangements of Cu 4 I 4 tetramers. The compounds with Cu 2 I 2 rhomboid dimers or Cu 4 I 4 cubane tetramers have higher photoluminescence quantum yields than those with Cu–I 1D chains and octahedral Cu 4 I 4 tetramers, owing to the optimal degree of condensation of the inorganic motifs, which suppresses nonradiative processes. Electronic structure calculations on these compounds point out the critical influence of the inorganic motif and organic ligand on the nature of the band gaps and thus the excitation characteristics. Temperature-dependent photoluminescence spectra are presented to better understand the nature of luminescence in compounds with different inorganic motifs. Here. the emerging understanding of composition–structure–property correlations in this family provides inspiration for the rational design of hybrid phosphors for general lighting applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A Structurally Diverse Compound Screening Library to Identify Substrates for Diamine, Polyamine, and Related Acetyltransferases

Spermidine/spermine N-acetyltransferases (SSATs) and other types of polyamine acetyltransferases (PAATs) acetylate diamines and/or polyamines. These enzymes are evolutionarily related and belong to the Gcn5-related N-acetyltransferase (GNAT) superfamily, yet we lack a fundamental understanding of their substrate specificity and/or promiscuity toward different compounds. Many of these enzymes are known or are predicted to acetylate polyamines, but in the cell there are other types of compounds that contain moieties derived from polyamines that may be the native substrates for these enzymes. To learn more about the identity of substrates that are acetylated, we selected and screened 17 different GNAT enzymes for activity toward a set of structurally diverse compounds that contained different types of amine moieties (e.g., aminopropyl, aminobutyl, etc.). These compounds included diamines, triamines, and polyamines containing primary amino groups, and they had structural diversity with variation of the chain length and presence or absence of internal amino groups and other functional groups. We found 12 of the 17 enzymes acetylated at least one of the compounds. Some enzymes were selective toward acetylating only one compound while others exhibited substrate promiscuity toward numerous compounds. Our experimental results ultimately allowed us to pinpoint specific substrates that could be further investigated to more fully understand substrate specificity versus promiscuity of GNAT enzymes and the role of acetylated small molecules in cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Exploring the Structural, Biochemical, and Functional Diversity of Glycoside Hydrolase Family 12 from Penicillium subrubescens

Glycoside hydrolases (GHs) play an essential role in plant biomass degradation and modification for the sustainable production of biochemicals. The filamentous Ascomycete fungus Penicillium subrubescens contains a higher number of GH12 candidates compared to related species. Therefore, we aimed to compare P. subrubescens GH12s for their ability and substrate specificity for plant cell wall polysaccharide degradation and species’ potential as a source of novel enzymes for plant biomass valorization. Our re-evaluated phylogenetic analysis of fungal GH12 members showed that the P. subrubescens GH12s were located in different (new) clades. Biochemical characterization marked PsEglA as an endoglucanase and four other P. subrubescens GH12s (i.e., PsXegA–D) as xyloglucanases. Interestingly, structural features of PsXegD and PsXegE were more comparable to those of Basidiomycete GH12 xyloglucanases with a unique open substrate-binding cleft. PsUegA displayed dual xyloglucanase and endoglucanase activity and also showed distinct structural features. Comparative transcriptome analysis supported the functional diversity of P. subrubescens GH12s in plant biomass degradation. The gene encoding PsUegA was expressed under diverse conditions, suggesting a scouting role for this enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Integration of Yeast Episomal/Integrative Plasmid Causes Genotypic and Phenotypic Diversity and Improved Sesquiterpene Production in Metabolically Engineered Saccharomyces cerevisiae

The variability in phenotypic outcomes among biological replicates in engineered microbial factories presents a captivating mystery. Establishing the association between phenotypic variability and genetic drivers is important to solve this intricate puzzle. Here, we applied a previously developed auxin-inducible depletion of hexokinase 2 as a metabolic engineering strategy for improved nerolidol production in Saccharomyces cerevisiae, and biological replicates exhibit a dichotomy in nerolidol production of either 3.5 or 2.5 g L –1 nerolidol. Harnessing Oxford Nanopore’s long-read genomic sequencing, we reveal a potential genetic cause—the chromosome integration of a 2μ sequence-based yeast episomal plasmid, encoding the expression cassettes for nerolidol synthetic enzymes. This finding was reinforced through chromosome integration revalidation, engineering nerolidol and valencene production strains, and generating a diverse pool of yeast clones, each uniquely fingerprinted by gene copy numbers, plasmid integrations, other genomic rearrangements, protein expression levels, growth rate, and target product productivities. Τhe best clone in two strains produced 3.5 g L –1 nerolidol and ~0.96 g L –1 valencene. Comparable genotypic and phenotypic variations were also generated through the integration of a yeast integrative plasmid lacking 2μ sequences. Our work shows that multiple factors, including plasmid integration status, subchromosomal location, gene copy number, sesquiterpene synthase expression level, and genome rearrangement, together play a complicated determinant role on the productivities of sesquiterpene product. Integration of yeast episomal/integrative plasmids may be used as a versatile method for increasing the diversity and optimizing the efficiency of yeast cell factories, thereby uncovering metabolic control mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Entropic Braiding Index ( eBI ): A Robust Metric to Account for the Diversity of Channel Scales in Multi‐Thread Rivers

Abstract The Braiding Index ( BI ), defined as the average count of intercepted channels per cross‐section, is a widely used metric for characterizing multi‐thread river systems. However, it does not account for the diversity of channels (e.g., in terms of water discharge) within different cross‐sections, omitting important information related to system complexity. Here we present a modification of BI, the Entropic Braiding Index ( eBI ), which augments the information content in BI by using Shannon Entropy to encode the diversity of channels in each cross section. eBI is interpreted as the number of “effective channels” per cross‐section, allowing a direct comparison with the traditional BI . We demonstrate the potential of the ratio BI/eBI to quantify channel disparity, differentiate types of multi‐thread systems (braided vs. anastomosed), and assess the effect of discharge variability, such as seasonal flooding, on river cross‐section stability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A New Coupled Biogeochemical Modeling Approach Provides Accurate Predictions of Methane and Carbon Dioxide Fluxes Across Diverse Tidal Wetlands

Abstract Tidal wetlands provide valuable ecosystem services, including storing large amounts of carbon. However, the net exchanges of carbon dioxide (CO 2 ) and methane (CH 4 ) in tidal wetlands are highly uncertain. While several biogeochemical models can operate in tidal wetlands, they have yet to be parameterized and validated against high‐frequency, ecosystem‐scale CO 2 and CH 4 flux measurements across diverse sites. We paired the Cohort Marsh Equilibrium Model (CMEM) with a version of the PEPRMT model called PEPRMT‐Tidal, which considers the effects of water table height, sulfate, and nitrate availability on CO 2 and CH 4 emissions. Using a model‐data fusion approach, we parameterized the model with three sites and validated it with two independent sites, with representation from the three marine coasts of North America. Gross primary productivity (GPP) and ecosystem respiration (R eco ) modules explained, on average, 73% of the variation in CO 2 exchange with low model error (normalized root mean square error (nRMSE) <1). The CH 4 module also explained the majority of variance in CH 4 emissions in validation sites ( R 2 = 0.54; nRMSE = 1.15). The PEPRMT‐Tidal‐CMEM model coupling is a key advance toward constraining estimates of greenhouse gas emissions across diverse North American tidal wetlands. Further analyses of model error and case studies during changing salinity conditions guide future modeling efforts regarding four main processes: (a) the influence of salinity and nitrate on GPP, (b) the influence of laterally transported dissolved inorganic C on R eco , (c) heterogeneous sulfate availability and methylotrophic methanogenesis impacts on surface CH 4 emissions, and (d) CH 4 responses to non‐periodic changes in salinity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Contribution of El Niño Southern Oscillation (ENSO) Diversity to Low‐Frequency Changes in ENSO Variance

Abstract El Niño Southern Oscillation (ENSO) diversity is characterized based on the longitudinal location of maximum sea surface temperature anomalies (SSTA) and amplitude in the tropical Pacific, as Central Pacific events are typically weaker than Eastern Pacific events. SSTA pattern and intensity undergo low‐frequency modulations, affecting ENSO prediction skill and remote impacts, and resulting in low‐frequency changes in ENSO variance. Yet, how different ENSO types contribute to these decadal variance changes remains unclear. Here, we decompose the low‐frequency changes of ENSO variance into contributions from ENSO diversity categories. We propose a fuzzy clustering of monthly SSTA to allow for non‐binary event category memberships, where each event can belong to different clusters. Our approach identifies two La Niña and three El Niño categories and shows that the major shift of ENSO variance in the mid‐1970s was associated with an increasing likelihood of strong La Niña and extreme El Niño events.

Geology↗
DOE OSTI2024

Quantifying the Diversity of an Atmospheric Aerosol Population in an Arctic Oil Field on a Single‐Particle Level

As the Arctic rapidly warms, sea ice extent is decreasing and oil and gas extraction activities are expanding. Local combustion emissions affect the Arctic atmospheric aerosol chemical mixing state (the distribution of chemical species across the aerosol population), which impacts climate-relevant properties. Bulk and single-particle measurements of submicron aerosols were conducted at Oliktok Point, Alaska within the North Slope of Alaska oil fields. In this work, we quantify aerosol diversity using online single-particle mass spectrometry data (32,880 individual particles), offline single-particle microscopy data (20,912 individual particles), and online bulk aerosol mass spectrometry and aethalometer data. This method was used to derive individual particle mass fractions for both refractory and non-refractory material within distinct particle types. Single-particle, average single-particle, and bulk population diversities (D i , D α , D γ , respectively) and mixing state indices (χ) were calculated for the data set. Calculated D i values were generally low (2.2 ± 0.6), as individual particle masses were dominated by a few chemical species of interest. Aged aerosol particles (those internally mixed with nitrate and/or sulfate) exhibited higher D i values (>3) compared to recently emitted (fresh) aerosol particles. During oil field plume periods, D α values approached three due to the abundance of diesel combustion particles, which were rich in sulfate, black carbon, and organic aerosol. Overall, the submicron aerosol population within the Arctic oil fields was found to be relatively externally mixed (χ < 50%), due to the constant local emissions within oil fields combining with background aerosol and locally emitted sea spray aerosol at the coastal site.

Wu, J.↗
DOE OSTI2021

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

Abstract Temperate phages are viruses of bacteria that can establish two types of infection: a lysogenic infection in which the virus replicates with the host cell without producing virions, and a lytic infection where the host cell is eventually destroyed, and new virions are released. While both lytic and lysogenic infections are routinely observed in the environment, the ecological and evolutionary processes regulating these viral dynamics are still not well understood, especially for uncultivated virus-host pairs. Here, we characterized the long-term dynamics of uncultivated viruses infecting green sulfur bacteria (GSB) in a model freshwater lake (Trout Bog Lake, TBL). As no GSB virus has been formally described yet, we first used two complementary approaches to identify new GSB viruses from TBL; one in vitro based on flow cytometry cell sorting, the other in silico based on CRISPR spacer sequences. We then took advantage of existing TBL metagenomes covering the 2005–2018 period to examine the interactions between GSB and their viruses across years and seasons. From our data, GSB populations in TBL were constantly associated with at least 2-8 viruses each, including both lytic and temperate phages. The dominant GSB population in particular was consistently associated with two prophages with a nearly 100% infection rate for >10 years. We illustrate with a theoretical model that such an interaction can be stable given a low, but persistent, level of prophage induction in low-diversity host populations. Overall, our data suggest that lytic and lysogenic viruses can readily co-infect the same host population, and that host strain-level diversity might be an important factor controlling virus-host dynamics including lytic/lysogeny switch.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Metabolically diverse microorganisms mediate methylmercury formation under nitrate-reducing conditions in a dynamic hydroelectric reservoir

Brownlee Reservoir is a mercury (Hg)-impaired hydroelectric reservoir that exhibits dynamic hydrological and geochemical conditions and is located within the Hells Canyon Complex in Idaho, USA. Methylmercury (MeHg) contamination in fish is a concern in the reservoir. While MeHg production has historically been attributed to sulfate-reducing bacteria and methanogenic archaea, microorganisms carrying the hgcA gene are taxonomically and metabolically diverse and the major biogeochemical cycles driving mercury (Hg) methylation are not well understood. In this study, Hg speciation and redox-active compounds were measured throughout Brownlee Reservoir across the stratified period in four consecutive years (2016–2019) to identify the location where and redox conditions under which MeHg is produced. Metagenomic sequencing was performed on a subset of samples to characterize the microbial community with hgcA and identify possible links between biogeochemical cycles and MeHg production. Biogeochemical profiles suggested in situ water column Hg methylation was the major source of MeHg. These profiles, combined with genome-resolved metagenomics focused on hgcA-carrying microbes, indicated that MeHg production occurs in this system under nitrate- or manganese-reducing conditions, which were previously thought to preclude Hg-methylation. Using this multidisciplinary approach, we identified the cascading effects of interannual variability in hydrology on the redox status, microbial metabolic strategies, abundance and metabolic diversity of Hg methylators, and ultimately MeHg concentrations throughout the reservoir. This work expands the known conditions conducive to producing MeHg and suggests that the Hg-methylation mitigation efforts by nitrate or manganese amendment may be unsuccessful in some locations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Structural diverseness of neurons between brain areas and between cases

The cerebral cortex is composed of multiple cortical areas that exert a wide variety of brain functions. Although human brain neurons are genetically and areally mosaic, the three-dimensional structural differences between neurons in different brain areas or between the neurons of different individuals have not been delineated. Here we report a nanometer-scale geometric analysis of brain tissues of the superior temporal gyrus of schizophrenia and control cases. The results of the analysis and a comparison with results for the anterior cingulate cortex indicated that (1) neuron structures are significantly dissimilar between brain areas and that (2) the dissimilarity varies from case to case. The structural diverseness was mainly observed in terms of the neurite curvature that inversely correlates with the diameters of the neurites and spines. The analysis also revealed the geometric differences between the neurons of the schizophrenia and control cases. The schizophrenia cases showed a thin and tortuous neuronal network compared with the controls, suggesting that the neuron structure is associated with the disorder. The area dependency of the neuron structure and its diverseness between individuals should represent the individuality of brain functions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Resolving the structure of phage–bacteria interactions in the context of natural diversity

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse—with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity

Enzymatic deconstruction of poly(ethylene terephthalate) (PET) is under intense investigation, given the ability of hydrolase enzymes to depolymerize PET to its constituent monomers near the polymer glass transition temperature. To date, reported PET hydrolases have been sourced from a relatively narrow sequence space. Here, we identify additional PET-active biocatalysts from natural diversity by using bioinformatics and machine learning to mine 74 putative thermotolerant PET hydrolases. We successfully express, purify, and assay 51 enzymes from seven distinct phylogenetic groups; observing PET hydrolysis activity on amorphous PET film from 37 enzymes in reactions spanning pH from 4.5–9.0 and temperatures from 30–70 °C. We conduct PET hydrolysis time-course reactions with the best-performing enzymes, where we observe differences in substrate selectivity as function of PET morphology. We employed X-ray crystallography and AlphaFold to examine the enzyme architectures of all 74 candidates, revealing protein folds and accessory domains not previously associated with PET deconstruction. Overall, this study expands the number and diversity of thermotolerant scaffolds for enzymatic PET deconstruction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Spatio-temporal dynamics of Hendra virus in Australia reveal stable maintenance of diverse viral clades among Pteropus bats

Hendra virus (HeV) was discovered in 1994 in Australia. Limited genomic data have hindered comprehensive understanding of HeV’s evolutionary dynamics. Here, in this work, we recovered 48 HeV genomes from bats and 9 from horses from Australia between 2016 and 2020, revealing four distinct clades. Each clade was distributed over a large spatial area with multiple clades co-circulating within a single bat roost on the same day and over consecutive years. The diversity and temporal stability of co-circulating clades suggest that viral dynamics are driven by episodic shedding of existing lineages maintained at the population level, rather than immune-driven strain-replacement dynamics. HeV isolates of different clades displayed variation in phenotypic properties but minimal antigenic differences. We provide an overview of evolutionary dynamics, phenotypic properties and assessment of countermeasures for HeV, and provide insights into the processes that maintain virus diversity in bats and influence the potential for viral emergence.

genetic variation↗
DOE OSTI2026

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current activity. This revealed an active mobilome that shapes natural genetic diversity via differential impacts on major phyla and affects a wide range of functions, including metabolic genes involved in carbon flux and nutrient cycling. These findings and this analytic framework suggest avenues towards a better understanding of MGE diversity, activity, mobility and impacts across ecosystems.

Biological and medical sciences↗
DOE OSTI2023

Large language models generate functional protein sequences across diverse families

Deep-learning language models have shown promise in various biotechnological applications, including protein design and engineering. Here, in this paper, we describe ProGen, a language model that can generate protein sequences with a predictable function across large protein families, akin to generating grammatically and semantically correct natural language sentences on diverse topics. The model was trained on 280 million protein sequences from >19,000 families and is augmented with control tags specifying protein properties. ProGen can be further fine-tuned to curated sequences and tags to improve controllable generation performance of proteins from families with sufficient homologous samples. Artificial proteins fine-tuned to five distinct lysozyme families showed similar catalytic efficiencies as natural lysozymes, with sequence identity to natural proteins as low as 31.4%. ProGen is readily adapted to diverse protein families, as we demonstrate with chorismate mutase and malate dehydrogenase.

59 BASIC BIOLOGICAL SCIENCES↗