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DOE OSTI2019

New insights from uncultivated genomes of the global human gut microbiome

The genome sequences of many species of the human gut microbiome remain unknown, largely owing to challenges in cultivating microorganisms under laboratory conditions. Here we address this problem by reconstructing 60,664 draft prokaryotic genomes from 3,810 faecal metagenomes, from geographically and phenotypically diverse humans. These genomes provide reference points for 2,058 newly identified species-level operational taxonomic units (OTUs), which represents a 50% increase over the previously known phylogenetic diversity of sequenced gut bacteria. On average, the newly identified OTUs comprise 33% of richness and 28% of species abundance per individual, and are enriched in humans from rural populations. A meta-analysis of clinical gut-microbiome studies pinpointed numerous disease associations for the newly identified OTUs, which have the potential to improve predictive models. Finally, our analysis revealed that uncultured gut species have undergone genome reduction that has resulted in the loss of certain biosynthetic pathways, which may offer clues for improving cultivation strategies in the future.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology

Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. Here, we propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant

Genital mycoplasmas, which can be vertically transmitted, have been implicated in preterm birth, neonatal infections, and chronic lung disease of prematurity. Our prior work uncovered 16S rRNA genes belonging to a novel, as-yet-uncultivated mycoplasma (lineage 'Mnola') in the oral cavity of a premature neonate. Here, we characterize the organism's associated community, growth status, metabolic potential, and population diversity. Sequencing of genomic DNA from the infant's saliva yielded 1.44 Gbp of high-quality, non-human read data, from which we recovered three essentially complete (including 'Mnola') and three partial draft genomes (including Trichomonas vaginalis). The completed 629,409-bp 'Mnola' genome (Candidatus Mycoplasma girerdii str. UC-B3) was distinct at the strain level from its closest relative, vaginally-derived Ca. M. girerdii str. VCU-M1, which is also associated with T. vaginalis. Replication rate measurements indicated growth of str. UC-B3 within the infant. Genes encoding surface-associated proteins and restriction-modification systems were especially diverse within and between strains. In UC-B3, the population genetic underpinnings of phase variable expression were evident in vivo. Unique among mycoplasmas, Ca. M. girerdii encodes pyruvate-ferredoxin oxidoreductase and may be sensitive to metronidazole. This study reveals a metabolically unique mycoplasma colonizing a premature neonate, and establishes the value of genome-resolved metagenomics in tracking phase variation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Metabolic Reconstruction and Modeling Microbial Electrosynthesis

Microbial electrosynthesis is a renewable energy and chemical production platform that relies on microbial cells to capture electrons from a cathode and fix carbon. Yet despite the promise of this technology, the metabolic capacity of the microbes that inhabit the electrode surface and catalyze electron transfer in these systems remains largely unknown. Here, we assembled thirteen draft genomes from a microbial electrosynthesis system producing primarily acetate from carbon dioxide, and their transcriptional activity was mapped to genomes from cells on the electrode surface and in the supernatant. This allowed us to create a metabolic model of the predominant community members belonging to Acetobacterium, Sulfurospirillum, and Desulfovibrio. According to the model, the Acetobacterium was the primary carbon fixer, and a keystone member of the community. Transcripts of soluble hydrogenases and ferredoxins from Acetobacterium and hydrogenases, formate dehydrogenase, and cytochromes of Desulfovibrio were found in high abundance near the electrode surface. Cytochrome c oxidases of facultative members of the community were highly expressed in the supernatant despite completely sealed reactors and constant flushing with anaerobic gases. The resulting molecular discoveries and metabolic modeling now serve as a foundation for future examination and development of electrosynthetic microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life

There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

A minimum information standard for reproducing bench-scale bacterial cell growth and productivity

Reproducing, exchanging, comparing, and building on each other’s work is foundational to technology advances. Advancing biotechnology calls for reliable reuse of engineered organisms. Reliable reuse of engineered organisms requires reproducible growth and productivity. Here, we identify the experimental factors that have the greatest effect on the growth and productivity of our engineered organisms in order to demonstrate reproducibility for biotechnology. Here, we present a draft of a Minimum Information Standard for Engineered Organism Experiments based on this method. We evaluate the effect of 22 factors on Escherichia coli engineered to produce the small molecule lycopene, and 18 factors on E. coli engineered to produce red fluorescent protein. Container geometry and shaking have the greatest effect on product titer and yield. We reproduce our results under two different conditions of reproducibility: conditions of use (different fractional factorial experiments), and time (48 biological replicates performed on 12 different days over four months).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

LAMP detection assays for boxwood blight pathogens: A comparative genomics approach

Rapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata , as well as three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. In conclusion, this comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.

1st report↗

DOE OSTI2017

Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation

The Candidate Phyla Radiation (CPR) is a large group of bacteria, the scale of which approaches that of all other bacteria. CPR organisms are inferred to depend on other community members for many basic cellular building blocks and all appear to be obligate anaerobes. To date, there has been no evidence for any significant respiratory capacity in an organism from this radiation. Here we report a curated draft genome for Candidatus Parcunitrobacter nitroensis' a member of the Parcubacteria (OD1) superphylum of the CPR. The genome encodes versatile energy pathways, including fermentative and respiratory capacities, nitrogen and fatty acid metabolism, as well as the first complete electron transport chain described for a member of the CPR. The sequences of all of these enzymes are highly divergent from sequences found in other organisms, suggesting that these capacities were not recently acquired from non-CPR organisms. Although the wide respiration-based repertoire points to a different lifestyle compared to other CPR bacteria, we predict similar obligate dependence on other organisms or the microbial community. The results substantially expand the known metabolic potential of CPR bacteria, although sequence comparisons indicate that these capacities are very rare in members of this radiation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

A Review of Crystalline Silicon Bifacial Photovoltaic Performance Characterisation and Simulation

Bifacial photovoltaic (PV) technology has received considerable attention in recent years due to the potential to achieve higher annual energy yield compared to its monofacial counterpart. Higher annual energy yield is a crucial factor (even more than to further reduce the module costs) because, with the use of higher power PV modules, the high BOS (Balance of System) costs can be reduced, resulting in the lowest LCOE (levelised cost of energy). The International Technology Roadmap for Photovoltaic (ITRPV) predicts an upward trend for the shares of crystalline silicon (c-Si) bifacial PV cells and modules in the global PV market in the next decade, i.e., more than 35% in 2028. Two key enabling factors have been identified to promote the widespread use of c-Si bifacial PV devices, namely the bifacial PV performance measurement method/standard for indoor characterisation and comprehensive simulation models for outdoor performance characterisation. Both will increase the bankability of bifacial PV technology. In this paper, a comprehensive review of the state-of-the-art of the c-Si bifacial PV performance characterisation and simulation is presented. First, an overview of the indoor characterisation of c-Si bifacial PV cells and modules is presented, followed by an overview of the outdoor characterisation of c-Si bifacial PV modules and the draft technical specification, IEC TS 60904-1-2. The second part of this paper reviews the current status of bifacial PV performance modelling, which includes the three primary sub-models: optical, electrical, and thermal models. This paper also provides an overview of the required future research to address the challenges associated with the characterisation and simulation of c-Si bifacial PV devices.

14 SOLAR ENERGY↗

DOE OSTI2024

Measurement of mix at the fuel–ablator interface in indirectly driven capsule implosions on the National Ignition Facility

The interface between the capsule ablator and fuel ice layer is susceptible to hydrodynamic instabilities. The subsequent mixing of hot ablator material into the ice reduces fuel compression at stagnation and is a candidate for reduced capsule performance. The ability to diagnose ice–ablator mix is critical to understanding and improving stability at this interface. Combining the crystal backlighter imager with the single line of sight camera on the National Ignition Facility (NIF) allows direct measurement of ice–ablator mix by providing multiple quasi-monochromatic radiographs of layered capsule implosions per experiment with high spatial (∼12 μm) and temporal (∼35 ps) resolution. The narrow bandwidth of this diagnostic platform allows radiography of the inner edge of the capsule limb close to stagnation without capsule self-emission contaminating the data and removes opacity uncertainties typically associated with the spectral content of the radiograph. Analysis of radiographic data via a parameterized forward-fitting Abel inversion technique provides measurements of the distribution of mix mass inwards from the ice–ablator interface. The sensitivity of this mix measurement technique was demonstrated by applying it to layered experiments in which the stability of the ice–ablator interface was expected to vary significantly. Additional experiments suggest that high-density carbon capsules that employ a buried-layer dopant profile suffer from mixing at the innermost doped–undoped interface. Data from these experiments suggest that opacity models used in hydrodynamic simulations of NIF experiments can potentially over-predict the opacity of doped capsules. LLNL-JRNL-850535-DRAFT.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2018

Determining Barotrauma in the Pictus Catfish, Pimelodus pictus, Experimentally Exposed to Simulated Hydropower Turbine Passage

Hydropower capacity is to be developed by 73% globally. This great development poses severe threats to the aquatic diversity and ecosystems services. Downstream passage of fish through turbines and the entrance at the draft tube are important impacts affecting the fish diversity. During such events, fish suffer rapid decompression, which can lead to barotrauma and mortality. Despite the magnitude of mortality events, data to understand barotrauma on fish is scarce and largely focused in salmonids. This study aimed to evaluate the effects of rapid decompression on the Amazonian benthic species Pimelodus pictus, simulated in hypo-hyperbaric chambers. All fish were negatively buoyant throughout the experiments, hindering the calculation of the ratio of pressure change and posing challenges to data analysis. Instead, the pressure of neutral buoyancy and time to decompression were used to establish the likelihood of barotrauma. The most frequent injuries in P. pictus were swim bladder rupture, intestine rupture, internal hemorrhage and embolism. The occurrence and magnitude of those injuries were related to the pressure of neutral buoyancy, pressure variation and time to decompression. Barotrauma studies with benthic fish species deemed to be challenging and are likely to require the use of complementary approaches on such species.

Do Vale Beirao, Bernardo↗

DOE OSTI2022

Diploid-dominant life cycles characterize the early evolution of Fungi

Most of the described species in kingdom Fungi are contained in two phyla, the Ascomycota and the Basidiomycota (subkingdom Dikarya). As a result, our understanding of the biology of the kingdom is heavily influenced by traits observed in Dikarya, such as aerial spore dispersal and life cycles dominated by mitosis of haploid nuclei. We now appreciate that Fungi comprises numerous phylum-level lineages in addition to those of Dikarya, but the phylogeny and genetic characteristics of most of these lineages are poorly understood due to limited genome sampling. Here, we addressed major evolutionary trends in the non-Dikarya fungi by phylogenomic analysis of 69 newly generated draft genome sequences of the zoosporic (flagellated) lineages of true fungi. Our phylogeny indicated five lineages of zoosporic fungi and placed Blastocladiomycota, which has an alternation of haploid and diploid generations, as branching closer to the Dikarya than to the Chytridiomyceta. Our estimates of heterozygosity based on genome sequence data indicate that the zoosporic lineages plus the Zoopagomycota are frequently characterized by diploid-dominant life cycles. We mapped additional traits, such as ancestral cell-cycle regulators, cell-membrane– and cell-wall–associated genes, and the use of the amino acid selenocysteine on the phylogeny and found that these ancestral traits that are shared with Metazoa have been subject to extensive parallel loss across zoosporic lineages. Together, our results indicate a gradual transition in the genetics and cell biology of fungi from their ancestor and caution against assuming that traits measured in Dikarya are typical of other fungal lineages.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force

Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Spectral and photochemical diversity of tandem cysteine cyanobacterial phytochromes

The atypical trichromatic cyanobacterial phytochrome NpTP1 from Nostoc punctiforme ATCC 29133 is a linear tetrapyrrole (bilin)-binding photoreceptor protein that possesses tandem-cysteine residues responsible for shifting its light-sensing maximum to the violet spectral region. Using bioinformatics and phylogenetic analyses, in this study we established that tandem-cysteine cyanobacterial phytochromes (TCCPs) compose a well-supported monophyletic phytochrome lineage distinct from prototypical red/far-red cyanobacterial phytochromes. To investigate the light-sensing diversity of this family, we compared the spectroscopic properties of NpTP1 (here renamed NpTCCP) with those of three phylogenetically diverged TCCPs identified in the draft genomes of Tolypothrix sp. PCC7910, Scytonema sp. PCC10023, and Gloeocapsa sp. PCC7513. Recombinant photosensory core modules of ToTCCP, ScTCCP, and GlTCCP exhibited violet-blue–absorbing dark-states consistent with dual thioether-linked phycocyanobilin (PCB) chromophores. Photoexcitation generated singly-linked photoproduct mixtures with variable ratios of yellow-orange and red-absorbing species. The photoproduct ratio was strongly influenced by pH and by mutagenesis of TCCP- and phytochrome-specific signature residues. Our experiments support the conclusion that both photoproduct species possess protonated 15E bilin chromophores, but differ in the ionization state of the noncanonical “second” cysteine sulfhydryl group. We found that the ionization state of this and other residues influences subsequent conformational change and downstream signal transmission. We also show that tandem-cysteine phytochromes present in eukaryotes possess similar amino acid substitutions within their chromophore-binding pocket, which tune their spectral properties in an analogous fashion. Taken together, our findings provide a roadmap for tailoring the wavelength specificity of plant phytochromes to optimize plant performance in diverse natural and artificial light environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

PWR Core Analysis for Cycle Extension and Uprates with LEU+ Accident Tolerant Fuel and 80 GWd/Tonne Burnup Limit

The U.S. Nuclear Regulatory Commission has recently drafted a rule enabling fuel burnup increase in light water reactors up to 80 GWd/t. In conjunction with use of fuel enrichment up to 10%, and accident tolerant fuel (ATF), this is anticipated to facilitate 24-month cycles in PWRs, along with further power uprates. In this paper, PWR core analysis is performed for 20% increased PWR power output along with cycle extension up to 24 months, in combination with use of chromia-doped fuel and chromium-coated clad, considered to be the most near-term ATF concepts. In combination, these lead to challenging conditions with a core average discharge burnup of up to ~74 GWd/t, challenging even the 80 GWd/t burnup limit. Analysis is performed using the 2-step method with POLARIS (within SCALE) used for the lattice calculations and PARCS for the core calculations. Core designs are first baselined for current operating conditions (LEU, 62 GWd/t discharge burnup limit) and then derived that meet cycle constraints on power distribution and the updated lead pin discharge burnup limit while maintaining at least two batches of fuel in the core. Gadolina loadings in fuel pins of up to 8% are used, with enrichment zoning both within the core and, to a limited extent, within assemblies. Here, doped fuel with coated cladding can utilize the same core designs as the reference UOX cores, exhibiting slightly lower burnup due to higher fuel density, which also offsets the slight reactivity penalty from the doping and coating. For the analysis performed here, doped fuel enabled a core with 24-month cycle and 20% uprate to stay within the 80 GWd/t lead pin discharge burnup limit.

LEU+↗

DOE OSTI2018

HEP Software Development in the Next Decade; the Views of the HSF Community

We have known for a while now that projections of computing needs for the experiments running in 10 years from now are unaffordable. Over the past year the HSF has convened a series of workshops aiming to find consensus on the needs, and produce proposals for research and development to address this challenge. At this time many of the software related drafts are far enough along to give a clear picture of what will result from this process. This talk will synthesize and report on some of the key elements to come out of this community work.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat

Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms, however little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity, and metabolic gradient measurements. Draft reconstructed genomes of abundant organisms revealed three dominant cyanobacterial populations differentially distributed across the top layers of the mat suggesting niche separation along light and oxygen gradients. Many organisms contained diverse functional profiles, allowing for metabolic response to changing conditions within the mat. Organisms with partial nitrogen and sulfur metabolisms were widespread indicating dependence upon metabolite exchange. In addition, changes in community spatial structure were observed over the diel. These results indicate that organisms within the mat community have adapted to the temporally dynamic environmental gradients in this hypersaline mat through metabolic flexibility and fluid syntrophic interactions, including shifts in spatial arrangements.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

The genome of the polyextremophilic yeast, Naganishia friedmannii, reveals adaptations involved in stress response pathways, carbohydrate metabolism expansion, and a limited DNA repair repertoire

Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derived carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.

Vimercati, Lara↗