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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

High Temperature Optocoupler for 3D High Density Power Modules

The goal of this proposed research is to develop a reliable high-temperature optocouplers, which can operate at 250°C with at least ten-year lifetime, and replace isolation transforms as the galvanic isolation solution for the 3D integration of high density power modules. The electrification of future transportations (i.e., electric vehicles) will continuously drive the demand for high density power modules. Optocouplers (i.e., packaged light emitter and detector) as a promising candidate to replace bulky isolation transformers are highly desirable to facilitate the continuous scale-down of gate driver circuitry that will lead to 3D high density power modules and achieve disruptive performance in terms of thermal management, power density, power efficiency, reliability and operating environments. However, regular semiconductor optoelectronic materials and devices have significant difficulty functioning in the harsh environments designated for high density power module usage (such as operation at high temperatures). Ultimately, it is not the intrinsic properties of power devices that prevent their use at higher temperatures, but rather the low voltage electronics needed to drive them and the packaging that surrounds them. The typical operating temperature for optocouplers is only up to 100°C, due to the limitations of light emitting diode (LED) devices inside and packaging materials. A systematic characterization methodology will be developed to analyze the performance, lifetime and reliability of LED devices and distinguish multiple failure mechanisms at high temperatures. An original methodology of “design for reliability” will be developed to design the optoelectronic devices with high reliability and long lifetime at high temperatures. A new architecture of high temperature high reliable optocouplers will be developed, fabricated and demonstrated with continuous operating at 250°C. The development of efficient, reliable high density 3D power modules is the foundation for energy efficiency and energy reliability. Enabled with advanced 3D integration and packaging technologies, high density power module solutions can achieve much more superior performance over the conventional discrete solutions in terms of efficiency, thermal management and power density. The proposed concept of high temperature optocouplers as the galvanic isolation solution for high density power modules will bring together interdisciplinary research involving the wide bandgap materials, optoelectronics, high reliable device design, electronics packaging and power modules. A streamline of skilled personnel would be trained including graduate and undergraduate students, local engineers and scientists which are in great demand to both academia and optoelectronics industry. The proposed research topics, such as, solid state lighting and high temperature device reliability, are currently of major interest at the Department of Energy, in particular, Sandia National Laboratories. This project can enhance collaborations between the University of Arkansas (UA) and Sandia National Laboratories. The findings of the proposed research are expected to be integrated into high density 3-D power modules at the Engineering Research Center for Power Optimization for Electro-Thermal Systems (POETS).

42 ENGINEERING↗
DOE OSTI2023

High-Throughput Directed Evolution of Marine Microalgae and Phototrophic Consortia for Improved Biomass Yields (Final Report)

Primary project achievements include using selective pressures (O 2 , light, temperature) and developing culturing regimes for the diatom Nitzschia inconspicua str. hildebrandi to attain enrichments with an ~90% increase in areal biomass productivity relative to the parental strain under pond-mimicking conditions with high O 2 stress in laboratory bioreactors. The resulting strain (GAI-337) was tested further for dilution time, culture density, CO 2 supplementation, pH, temperature, and dissolved O 2 concentration under outdoor pond-mimicking conditions to improve areal productivities. These experiments yielded an optimum harvest and dilution time just after sunset, ~0.45 g AFDW L -1 initial culture density for maximal productivities, no requirement for CO 2 supplementation or pH control, maximal performance under a diel temperature curve going from 24 °C at night to 36 °C during the day, and benefits from some O 2 removal from the culture by bubbling with air. Using pond-mimicking laboratory bioreactors, N. inconspicua GAI-337 achieved ~42 g AFDW m -2 d -1 . Nutrient limitation experiments resulted in a biomass composition that equated to ~160 Gallons of Gasoline Equivalent energy per ton AFDW, highlighting the potential of GAI-337 as a promising renewable fuel feedstock strain. Genome resequencing has revealed genome alterations potentially contributing to the improved growth of GAI-337 in the laboratory. Based on the comparative analyses of the GAI-337 and GAI-229 (reference) strains, we identified 144 single nucleotide substitutions that resulted in amino acid change, 7 single nucleotide substitutions that resulted in protein truncation; 5 deletions; and 1 frameshift mutation. From the mutations that potentially affect expression of functionally annotated genes, particular interest was noted for an interferon-induced 6-16 family protein that may be involved in the host immune response against microbe invasion; the chaperone protein DnaK, which may function to protect the folding of proteins within the cell; and SPRY domain protein that is found in many eukaryotic proteins important in cell signaling pathways. Transcriptome analysis revealed over 1000 genes with increased transcript levels. Many of these and many of the genes with mutations are not yet functionally annotated and an increased bioinformatics effort is necessary to more completely analyze the Nitzschia inconspicua genome. Adaptive laboratory evolution (ALE) was performed for over 300 days using consecutive 0.5°C temperature increases in a constant temperature incubator to attain greater thermal tolerance in Nitzschia inconspicua. The adapted strain was able to grow at a constant temperature of 37.5°C; whereas this constant temperature was lethal to the parental control, which had an upper temperature boundary of 35.5°C prior to adaptive evolution. Several high-temperature clonal isolates were obtained from the evolved population following ALE, and increased temperature tolerance was observed in clonal adapted cultures. The final temperature adaptation was maintained through cryopreservation and was observed in multiple clonal isolates, including multiple clonal isolates with significantly increased cell size, indicating the potential occurrence of a sexual cycle during the clonal isolation process. A survey of Nannochloropsis strains was conducted for tolerances to high pH and high bicarbonate media. Nannochloropsis granulata showed promising growth in diel bioreactors and was successfully grown at the GAI Kauai farm site in long-term growth campaigns. Co-culturing using Nitzschia inconspicua, Nannochloropsis and a cyanobacterium were assembled in the laboratory to determine if productivity synergies could be attained. Although all strains grew well in the laboratory high-bicarbonate media individually, the cyanobacterium quickly outgrew the other strains in the laboratory consortium pushing the co-culture away from a diverse (and potentially synergistic assemblage) phototroph culture towards a monoculture dominated by the cyanobacterium. Several outdoor growth campaigns were conducted, with productivities ranging between 10-20 g/m 2 /d of biomass. The best performing strain in the laboratory (GAI-337) did not outperform reference strains at the Kauai farm under the conditions used. Addition growth campaigns are necessary under conditions that result in higher biomass (>20 g/m 2 /d) and that attain higher O 2 levels are likely necessary. Initial data indicate that the thermally adapted strain did slightly better than the control strain at higher temperatures; however, additional campaigns are necessary to establish statistical significance. In summary, Nitzschia inconspicua is able to attain exemplary biomass and lipid yields in the laboratory bioreactors. Strain evolution to both O 2 and temperature resulted in targeted strain improvements. Additional outdoor campaigns are necessary to determine if laboratory improvements translate to the field.

09 BIOMASS FUELS↗
DOE OSTI2023

Metabacillus indicus EGFCL74

Chromosomal DNA of bacterium isolated from fermented cider (originally named m74) was sequenced on an Illumina NovaSeq platform 2x150bp. Raw paired end reads were trimmed and processed with BBDUK v39.01. Trimmed FASTQ files were uploaded to the KBase narrative. Within KBase, the paired-end reads were assembled using SPAdes v3.15.3 (output data file m74_SPAdes.Assembly). Completeness was evaluated with CheckM v1.0.18. The assembled genome was annotated using RAStk v1.073 (output data file m74_RAStkgenomeassembly). Comparison of the isolate genome to other available genomes was performed two ways. The InsertGenomeIntoSpeciesTree function placed the isolate in the same clade as Bacillus indicus (later renamed Metabacillus indicus). FastANI was then used to compare the average nucleotide identity of isolate (m74) to 3 available strains of Metabacillus indicus (ASM70993v2, ASM70875v2, 4-1317).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Combinatorial library design for improving isobutanol production in Saccharomyces cerevisiae

Saccharomyces cerevisiae is the dominant fermentative producer of ethanol in industry and a preferred host for production of other biofuels. That said, rewiring the metabolism of S. cerevisiae to produce other fermentation products, such as isobutanol, remains an academic challenge. Many studies report aerobic production of isobutanol, but ethanol remains a substantial by-product under these conditions due to the Crabtree effect. These studies indicate that the native isobutanol pathway is incapable of carrying sufficient flux to displace ethanol. In this report, we screened a combinatorial library of pathway enzymes to identify an isobutanol pathway cassette capable of supporting the growth of a non-ethanol producing S. cerevisiae . We began by identifying a diverse set of isobutanol pathway enzyme homologs and combined each open reading frame with varied-strength promoters in a combinatorial, pooled fashion. We applied a growth-coupled screen where a functional isobutanol pathway restored NAD + regeneration during glucose catabolism that is otherwise repressed via the Crabtree effect. Using this screen, we isolated a cassette consisting of a mosaic of bacterial and cytosol-localized fungal enzymes that conferred under aerobic conditions the ability to produce 364 mg/L isobutanol (8.8% of the theoretical maximum yield). We next shifted the cofactor usage of the isolated ketol-acid reductoisomerase enzyme in the cassette from NADPH to NADH-preferring to improve redox balance. The approach used herein isolated isobutanol producing strains that approach the best in the literature without producing substantial ethanol titers. Still, the best isolated cassette was insufficient to support anaerobic growth in the absence of ethanol fermentation - indicating the presence of further fundamental gaps in our understanding of yeast fermentation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Evidence of Asexual Overwintering of Melampsora paradoxa and Mapping of Stem Rust Host Resistance in Salix

Melampsora rust is a devastating disease of shrub willow in North America. Previous work has identified Melampsora paradoxa as one of two identified rust species in New York State that infect Salix purpurea and other important Salix host species, however little is known about the population of this rust species in this region. Genotyping-by-sequencing was used to identify single nucleotide polymorphisms (SNPs) and assess population diversity of M. paradoxa isolates collected from three Salix breeding populations in Geneva, NY between 2015 and 2020. Statistical analyses of SNP revealed that all isolates collected were clonally derived even though they were collected across years. In 2020, isolates were collected from stem infections where uredospore pustules were observed, and these isolates were also identical to M. paradoxa collected in previous seasons. These data suggest that M. paradoxa sampled across multiple years overwintered and reproduced asexually and that stem infection is a possible mechanism for overwintering, both of which are novel findings for this rust species. Additionally, field disease ratings were conducted on a S. purpurea × S. suchowensis F 1 breeding population with high disease severity, enabling the discovery of QTL for resistance on chromosomes 1 and 19. Lastly, Colletotrichum salicis was frequently associated with stem rust and may play a role in M. paradoxa stem infection. Together, this work is the first substantial exploration into M. paradoxa population biology, stem infection, and host resistance in Salix.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The SAGA Survey. V. Modeling Satellite Systems around Milky Way–Mass Galaxies with Updated UniverseMachine

Abstract Environment plays a critical role in shaping the assembly of low-mass galaxies. Here, we use the U niverse M achine (UM) galaxy–halo connection framework and Data Release 3 of the Satellites Around Galactic Analogs (SAGA) Survey to place dwarf galaxy star formation and quenching into a cosmological context. UM is a data-driven forward model that flexibly parameterizes galaxy star formation rates (SFRs) using only halo mass and assembly history. We add a new quenching model to UM, tailored for galaxies with m ⋆ ≲ 10 9 M ⊙ , and constrain the model down to m ⋆ ≳ 10 7 M ⊙ using new SAGA observations of 101 satellite systems around Milky Way (MW)–mass hosts and a sample of isolated field galaxies in a similar mass range from the Sloan Digital Sky Survey. The new best-fit model, “UM-SAGA,” reproduces the satellite stellar mass functions, average SFRs, and quenched fractions in SAGA satellites while keeping isolated dwarfs mostly star-forming. The enhanced quenching in satellites relative to isolated field galaxies leads the model to maximally rely on halo assembly to explain the observed environmental quenching. Extrapolating the model down to m ⋆ ∼ 10 6.5 M ⊙ yields a quenched fraction of ≳30% for isolated field galaxies and ≳80% for satellites of MW-mass hosts at this stellar mass. Spectroscopic surveys can soon test this specific prediction to reveal the relative importance of internal feedback, cessation of mass and gas accretion, satellite-specific gas processes, and reionization for the evolution of faint low-mass galaxies.

Wang, Yunchong (ORCID:000000018913626X)↗
DOE OSTI2025

The SAGA Survey. VI. The Size–Mass Relation for Low-mass Galaxies Across Environments

We investigate how Milky Way (MW)–like environments influence the sizes and structural properties of low mass galaxies by comparing satellites of MW analogs from the Satellites Around Galactic Analogs (SAGA) Survey with two control samples: an environmentally agnostic population from the SAGA background sample and isolated galaxies from the Sloan Digital Sky Survey NASA-Sloan Atlas. All sizes and structural parameters are measured uniformly using pysersic to ensure consistency across samples. We find the half-light sizes of SAGA satellites are systematically larger than those of isolated galaxies, with the magnitude of the offset ranging from 0.05 to 0.12 dex (10%–24%) depending on the comparison sample and completeness cuts. This corresponds to physical size differences between 85 and 200 pc at log 10 (M$_{{\star}}$/M ⊙ ) = 7.5 and 220–960 pc at log 10 (M$_{{\star}}$/M ⊙ ) = 10. This offset persists among star-forming galaxies, suggesting that environment can influence the structure of low-mass galaxies even before it impacts quenching. The intrinsic scatter in the size–mass relation is lower for SAGA satellites than isolated galaxies, and the Sérsic index distributions of satellites and isolated galaxies are similar. In comparison to star-forming satellites, quenched SAGA satellites have a slightly shallower size–mass relation and rounder morphologies at low mass, suggesting that quenching is accompanied by structural transformation and that the processes responsible differ between low- and high-mass satellites. Our results show that environmental processes can imprint measurable structural differences on satellites in MW-mass halos.

Asali, Yasmeen [Yale Univ., New Haven, CT (United ↗
DOE OSTI2021

Development of an inexpensive matrix-assisted laser desorption—time of flight mass spectrometry method for the identification of endophytes and rhizobacteria cultured from the microbiome associated with maize

Many endophytes and rhizobacteria associated with plants support the growth and health of their hosts. The vast majority of these potentially beneficial bacteria have yet to be characterized, in part because of the cost of identifying bacterial isolates. Matrix-assisted laser desorption-time of flight (MALDI-TOF) has enabled culturomic studies of host-associated microbiomes but analysis of mass spectra generated from plant-associated bacteria requires optimization. In this study, we aligned mass spectra generated from endophytes and rhizobacteria isolated from heritage and sweet varieties of Zea mays. Multiple iterations of alignment attempts identified a set of parameters that sorted 114 isolates into 60 coherent MALDI-TOF taxonomic units (MTUs). These MTUs corresponded to strains with practically identical (>99%) 16S rRNA gene sequences. Mass spectra were used to train a machine learning algorithm that classified 100% of the isolates into 60 MTUs. These MTUs provided >70% coverage of aerobic, heterotrophic bacteria readily cultured with nutrient rich media from the maize microbiome and allowed prediction of the total diversity recoverable with that particular cultivation method. Acidovorax sp., Pseudomonas sp. and Cellulosimicrobium sp. dominated the library generated from the rhizoplane. Relative to the sweet variety, the heritage variety contained a high number of MTUs. The ability to detect these differences in libraries, suggests a rapid and inexpensive method of describing the diversity of bacteria cultured from the endosphere and rhizosphere of maize.

dereplication↗
DOE OSTI2020

Separation of High Purity Oxygenated Aromatics from Catalytic Fast Pyrolysis Organic Streams

Thermochemical conversion of lignocellulosic biomass offers an attractive route to produce fuels and chemicals. Specifically, catalytic fast pyrolysis (CFP) oils have been shown to contain a high concentration of oxygenated aromatics, which can be isolated as value-added co-products. Purification of oxygenated aromatics can be a viable pathway to more economically competitive biorefineries, yet the isolation of highly pure coproduct streams remains technically challenging due to the high chemical heterogeneity of thermochemical process steams. Here, we demonstrate an industrially scalable process for isolating phenol, a widely used precursor to plastics, from CFP oil. Importantly, we leverage standard industrial processes, such as distillation, liquid-liquid extraction, and crystallization, to achieve phenol with 97% purity. In addition, the primary distillation of the CFP oil yielded several other fractions that contain chemicals with the potential to be isolated (e.g. cyclic ketones, cresols, and guaiacols). This work provides a technically feasible path to high purity oxygenated aromatics that has the potential to offset fuel production costs in a biorefinery.

09 BIOMASS FUELS↗
DOE OSTI2022

Recovering Native-Like Lignin from Poplar Biomass Using Flow-Through Solvolysis

Lignin valorization, frequently involving a depolymerization step, is necessary for economic production of lignocellulosic biofuels. However, isolation of lignin frequently degrades the structure such that depolymerization yields from the isolated lignin are decreased relative to the "native" lignin present in the plant. In this work we show that by using flow-through extraction with methanol at 225 degrees C, combined with rapid quenching, we can isolate a "native-like" lignin that produces monomer yields comparable the lignin in the parent biomass under reductive catalytic fractionation (RCF) conditions. This isolated, native-like lignin is shelf-stable at room temperature on a time scale of months, and can be concentrated to a lignin oil and reconstituted in methanol without losing activity. These features will facilitate the study of intrinsic lignin properties and steady-state depolymerization processes.

BIOMASS FUELS↗
DOE OSTI2020

Ga speciation in Ga/H-ZSM-5 by in-situ transmission FTIR spectroscopy

H-ZSM-5 supported Ga (Ga/H-ZSM-5) has long been recognized as a promising catalyst for nonoxidative dehydrogenation and dehydroaromatization of alkanes. However, Ga speciation under reaction conditions remains controversial. In this work, in-situ transmission Fourier Transform infrared (FTIR) spectroscopy is employed to systematically investigate Ga speciation in Ga/H-ZSM-5 with three Si/Al ratios (15, 28 and 39) and a wide range of Ga/Al ratios (0–1.7). Quantitative FTIR spectroscopy with pyridine reveals that one Ga atom roughly replaces one Brønsted acid site (BAS) at Ga/BAS ratio up to 0.7, however, only up to ~80% of the BAS on the H-ZSM-5 can be exchanged even with excess amounts of Ga. At a low Si/Al ratio of 15, the intensity of GaH x bands on reduced Ga/H-ZSM-5 at 550 °C increases almost linearly at low Ga loadings (Ga/Al < 0.13), and then levels off. In contrast, no detectable GaH x bands are observed on Ga/H-ZSM-5 with a high Si/Al ratio of 39, with Ga/Al ratios up to 1.3. The dependence of GaH x bands on both the Si/Al ratios and the Ga/Al ratios shows that Ga speciation varies with BAS density in the zeolite. We hypothesize that paired BAS sites are preferentially exchanged with Ga + , leading to the formation of Ga + –H + pair sites, while the exchange of isolated BAS form isolated Ga+ species. Using water as a probe molecule, we show that isolated Ga + and Ga + –H + pair sites have distinct properties, i.e., the former can be easily oxidized by water at 150 °C to form GaOOH species, while the latter is inactive under the same conditions. Furthermore, these results provide direct experimental evidence for the existence of two types of Ga species on reduced Ga/H-ZSM-5, highlighting the possibility that they have different catalytic activities in alkane dehydrogenation reactions.

03 NATURAL GAS↗
DOE OSTI2025

Integrating HPC simulations and physical experiments to characterize the effects of gamma radiation on seismic protective devices

Seismic protective systems, composed of seismic isolators and dampers, can substantially reduce the effects of earthquake shaking on nuclear power plants and components therein. To enable the use of these devices to protect equipment inside a plant and close to a source of radiation, the U.S. Department of Energy (DOE) funded a project at the Idaho National Laboratory (INL) and the University at Buffalo to characterize the effects of absorbed gamma dose on their mechanical properties. An early task in the project was to determine the exposure time required in the INL Foss Therapy Services (FTS) 60 Co gamma irradiator to achieve a target absorbed dose in the materials used to construct isolators and dampers, including fluids, polymers, composites, and metals. This task required the novel integration of high-performance computing (HPC), Monte Carlo N-Particle (MCNP) simulations, and irradiation experiments using Fricke dosimetry. An MCNP model of the FTS irradiator at INL was developed and validated using Fricke dosimetry. Simulations of three experiments in the irradiator, two with Fricke vials only and one with Fricke vials and a large-size isolator, predicted the Fricke-measured absorbed dose rate to within 15% in all three cases, providing high confidence in the calculation of the gamma dose absorbed in the materials comprising the seismic protective devices. The simulations demonstrated that the effects of photon scattering on absorbed dose rate in the FTS irradiator are negligible for test articles installed close to the cobalt sources and near the rear of the irradiator. The validated MCNP model of the FTS irradiator is being used to support ongoing DOE-funded experiments on seismic protective devices and could be applied to future, non-seismic-related experiments. In conclusion, the novel validation process successfully deployed for the FTS irradiator at INL could be applied to other irradiators, requiring new MCNP models and simulations, and irradiation experiments using dosimeters.

42 - ENGINEERING↗
DOE OSTI2023

Phyllosphere exudates select for distinct microbiome members in sorghum epicuticular wax and aerial root mucilage

Phyllosphere exudates create specialized microhabitats that shape microbial community diversity. We explored the microbiome associated with two sorghum phyllosphere exudates, the epicuticular wax and aerial root mucilage. We assessed the microbiome associated with the wax from sorghum plants over two growth stages, and the root mucilage additionally from nitrogen-fertilized and non-fertilized plants. In parallel, we isolated and characterized hundreds of bacteria from wax and mucilage, and integrated data from cultivation-independent and cultivation-dependent approaches to gain insights into exudate diversity and bacterial phenotypes. We found that Sphingomonadaceae and Rhizobiaceae families were the major taxa in the wax regardless of water availability and plant developmental stage to plants. The cultivation-independent mucilage-associated bacterial microbiome contained Erwiniaceae, Flavobacteriaceae, Rhizobiaceae, Pseudomonadaceae, Sphingomonadaceae, and its structure was strongly influenced by sorghum development but only modestly influenced by fertilization. In contrast, the fungal community structure of mucilage was strongly affected by the year of sampling but not by fertilization or plant developmental stage, suggesting a decoupling of fungal-bacterial dynamics in the mucilage. Our bacterial isolate collection from wax and mucilage had several isolates that matched 100% to detected amplicon sequence variants, and were enriched on media that selected for phenotypes including phosphate solubilization, putative diazotrophy, resistance to desiccation, capability to grow on methanol as a carbon source, and ability to grow in the presence of linalool and β-caryophyllene (terpenes in sorghum wax). This work expands our understanding of the microbiome of phyllosphere exudates and supports our long-term goal to translate microbiome research to support sorghum cultivation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Utah FORGE 10-3726: Geothermal Multiset Straddle for High Temperature Applications - 2024 Annual Workshop Presentation

This is a presentation on the Geothermal Multiset Straddle (GMS) for High Temperature Applications by Welltec, presented by Ricardo Vasques. This video slide presentation discusses the development of (1) an annular multiset isolation system; (2) a stimulation straddle isolation system; and (3) a multi open-close flow system, for geothermal environments. This is to enable effective zonal isolation and stimulation with multiset capabilities, to implement downhole controlled EGS in any location, and to extend the productive life of the well. This presentation was featured in the Utah FORGE R&D Annual Workshop on August 15, 2024.

15 GEOTHERMAL ENERGY↗
DOE OSTI2025

Complete genome sequence of Sphingobium yanoikuyae strain CC4533

We have isolated a new strain of Sphingobium yanoikuyae , which belongs to the class Alphaproteobacteria, order Sphingomonadales, and family Sphingomonadaceae. This carotenoid-producing strain is capable of degrading xenobiotics and is tolerant to toxic levels of six heavy metals. We have designated the newly isolated strain of S. yanoikuyae as S. yanoikuyae strain CC4533 (hereafter called strain CC4533) because it was isolated from a contaminated Tris-Acetate-Phosphate (TAP) medium culture plate of a green micro-alga Chlamydomonas reinhardtii wild type strain CC4533. We sequenced the whole genome of strain CC4533 using the PacBio Sequel II Continuous Long Read technology and have submitted it to NCBI along with the SRA and PacBio methylation motif data. Additionally, we have submitted the PacBio methylome to REBASE, Ref#35996. We present the whole genome sequence of S. yanoikuyae strain CC4533 that offers insights into its coding and non-coding genes and its nearest taxonomic neighbors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Culturing of “Unculturable” Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater

Recovery and cultivation of diverse environmentally-relevant microorganisms from the terrestrial subsurface remain a challenge despite recent advances in modern molecular technology. Here, we applied complex carbon (C) sources, i.e., sediment dissolved organic matter (DOM) and bacterial cell lysate, to enrich groundwater microbial communities for 30 days. As comparisons, we also included enrichments amended with simple C sources including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex C is far more effective in enriching diverse and distinct microorganisms from groundwater than simple C. Simple C enrichments yield significantly lower biodiversity, and are dominated by few phyla (e.g., Proteobacteria and Bacteroidetes ), while microcosms enriched with complex C demonstrate significantly higher biodiversity including phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia , Planctomycetes , and Armatimonadetes ). Subsequent isolation from complex C enrichments yielded 228 bacterial isolates representing five phyla, 17 orders, and 56 distinct species, including candidate novel, rarely cultivated, and undescribed organisms. Results from this study will substantially advance cultivation and isolation strategies for recovering diverse and novel subsurface microorganisms. Obtaining axenic representatives of “once-unculturable” microorganisms will enhance our understanding of microbial physiology and function in different biogeochemical niches of terrestrial subsurface ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Survey of Thirteen Novel Pseudomonas putida Bacteriophages

Bacteriophages have been widely investigated as a promising treatment of food, medical equipment, and humans colonized by antibiotic-resistant bacteria. Phages pose particular interest in combating those bacteria which form biofilms, such as the medically important human pathogen Pseudomonas aeruginosa and several plant pathogens, including P. syringae . In an undergraduate lab course, P. putida was used as the host to isolate novel anti-pseudomonal bacteriophages. Environmental samples of soil and water were collected, and purified phage isolates were obtained. After Illumina sequencing, genomes of these phages were assembled de novo and annotated. Assembled genomes were compared with known genomes in the literature and GenBank to identify taxonomic relations and to refine their functional annotations. The thirteen phages described are sipho-, myo-, and podoviruses in several families of Caudoviricetes , spanning several novel genera, with genomes ranging from 40,000 to 96,000 bp. One phage (DDSR119) is unique and is the first reported P. putida siphovirus. The remaining 12 can be clustered into four distinct groups. Six are highly related to each other and to previously described Autotranscriptaviridae phages: Waldo5, PlaquesPlease, and Laces98 all belong to the Waldovirus genus, whereas Stalingrad, Bosely, and Stamos belong to the Troedvirus genus. Zuri was previously classified as the founding member of a new genus Zurivirus within the family Schitoviridae . Ebordelon and Holyagarpour each represent different species within Zurivirus , whereas Meara is a more distantly related member of the Schitoviridae . Dolphis and Jeremy are similar enough to form a genus but have only a few distant relatives among sequenced phages and are notable for being temperate. We identified the lysis cassettes in all 13 phages, compared tail spike structures, and found auxiliary metabolic genes in several. Studies like these, which isolate and characterize infectious virions, enable the identification of novel proteins and molecular systems and also provide the raw materials for further study, evaluation, and manipulation of phage proteins and their hosts.

Pseudomonas putida↗