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DOE OSTI2022

Bioconversion and quantification of humic substances from low rank coals using indigenous fungal isolates

The major portion of coals around the world belongs to lignitic origin, and burning of these Low Rank Coals (LRCs) not only produces energy, but also release harmful gases into the environment. On the other hand, coal is a mega source of fossilized carbon compounds that can be utilized in diverse range of carbon/organic industries. Biosolubilization is one of the safest and economical way to consume these LRCs for the harvest of humic and fulvic acids for industrial applications. Present studies deal with solubilization of coal samples from five different mines of Punjab, Pakistan by indigenously isolated fungus. From a number of indigenously isolated fungal isolates, an isolate NF-2 was selected based on its solubilization potential on solid Sabouraud medium. The intensity of coal biosolubilization was found maximum for coal sample B-1 (59%) and lowest for sample B-26 (17.2%) with 5% (w/v) pulp density at 28 ± 2°C. Humification index value (A 4 /A 6 ) for biosolubilized products of coal sample B-1 was found 6.18 which was much higher than the A 4 /A 6 value (4.27) of commercially available standard humic acid. Biosolubilized products from coal sample B-1 was found maximum with 8681 mg/L humic acid concentration as determined by standard curve method. FTIR and FE-SEM analyses of sample B-1 treated with NF-2 confirmed the structural break down and solubilization of coal. Molecular identification of fungal isolate NF-2 showed 100% similarity to Aspergillus flavus. Here, this work paves the way to utilize lignitic coals for the environment friendly and low-cost production of humic acids by fungal biosolubilization as an alternate to chemical methods.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Modeling of surface-state induced inter-electrode isolation of n -on- p devices in mixed-field and γ -irradiation environments

Position sensitive n-on-p silicon sensors will be utilized in the tracker and in the High Granularity Calorimeter (HGCAL) of the Compact Muon Solenoid (CMS) experiment at High Luminosity Large Hadron Collider (HL-LHC). The detrimental effect of the radiation-induced accumulation of positive net oxide charge on position resolution in n-on-p sensors has typically been countered by the application of isolation implants like p-stop or p-spray between n + -electrodes. In addition to the positively charged layer inside the oxide and close to the Si/SiO 2 -interface, surface damage introduced by ionizing radiation in SiO 2 -passivated silicon particle detectors includes the accumulation of trapped-oxide-charge and interface traps. A previous study of either n/γ (mixed field)- or γ-irradiated Metal-Oxide-Semiconductor (MOS) capacitors showed evidence of substantially higher introduction rates of acceptor- and donor-type deep interface traps (N it,acc/don ) in mixed-field environment. Here, in this work, an inter-pad and -strip resistance (or resistivity (ρ int )) simulation study of n-on-p sensors with and without p-stop isolation implants was conducted for both irradiation types. Higher levels of ρint showed correlation to higher densities of deep N it,acc/don , with the inter-pad isolation performance of the mixed-field irradiated sensors becoming independent of the presence of p-stop implant between the n + - electrodes up to about 100 kGy. The low introduction rates of deep N it,acc/don in γ-irradiated sensors resulted in high sensitivity of ρ int to the presence and peak doping of p-stop above the lowest dose of about 7 kGy in the study. As a consequence of the advantageous influence of radiation-induced accumulation of deep N it on the inter-electrode isolation, position sensitive n-on-p sensors without isolation implants may be considered for future HEP-experiments where the radiation is largely due to hadrons.

Akchurin, N. [Texas Tech Univ., Lubbock, TX (Unite↗

DOE OSTI2022

Isolating intermediate Mg 11 Cu 6 Al 12 phase in ternary Mg-Cu-Al alloy by electrolytic dealloying

While dealloying is widely used to create nanoporous materials, it has rarely been employed to isolate difficult-to-synthesize intermediate phases. Here, in this work, we show how air-free, electrolytic dealloying at room temperature can be used to isolate the ternary intermetallic Mg 11 Cu 6 Al 12 phase. We create a ternary Mg-Cu-Al parent alloy containing the Mg 11 Cu 6 Al 12 compound and other phases, then subsequently remove these other phases via electrolytic dealloying to isolate the Mg 11 Cu 6 Al 12 phase. Isolated Mg 11 Cu 6 Al 12 phase exhibits ≈1 μm diameter rod-shaped microstructure. Phase and chemical analysis conducted using various techniques, including inductively coupled plasma and lab and synchrotron-based X-ray diffraction, show minimal impurities. This new approach to isolate the Mg 11 Cu 6 Al 12 phase can unlock its use in fundamental research and can be applied to other difficult-to-synthesize intermetallic compounds.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%–50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Soil microbiomes harbour unparalleled functional and phylogenetic diversity. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. As methylation was proposed to be catalysed by sulfate-reducing bacteria. However, to date, there are no available anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harbouring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Genomic description of human clinical Aspergillus fumigatus isolates, California, 2020

Abstract Aspergillus fumigatus, an environmental mold, causes life-threatening infections. Studies on the phylogenetic structure of human clinical A. fumigatus isolates are limited. Here, we performed whole genome sequencing of 24 A. fumigatus isolates collected from 18 patients in U.S. healthcare facilities in California. Single-nucleotide polymorphism (SNP) differences between patient isolates ranged from 187 to 70 829 SNPs. For five patients with multiple isolates, we calculated the within-host diversities. Three patients had a within-host diversity that ranged from 4 to 10 SNPs and two patients ranged from 2 to 16 977 SNPs. Findings revealed highly diverse A. fumigatus strains among patients and two patterns of diversity for isolates that come from the same patient, low and extremely high diversity.

Misas, Elizabeth (ORCID:0000000162437716)↗

DOE OSTI2023

Chicken Production and Human Clinical Escherichia coli Isolates Differ in Their Carriage of Antimicrobial Resistance and Virulence Factors

Contamination of food animal products by Escherichia coli is a leading cause of foodborne disease outbreaks, hospitalizations, and deaths in humans. Chicken is the most consumed meat both in the United States and across the globe according to the U.S. Department of Agriculture. Although E. coli is a ubiquitous commensal bacterium of the guts of humans and animals, its ability to acquire antimicrobial resistance (AMR) genes and virulence factors (VFs) can lead to the emergence of pathogenic strains that are resistant to critically important antibiotics. Thus, it is important to identify the genetic factors that contribute to the virulence and AMR of E. coli. In this study, we performed in-depth genomic evaluation of AMR genes and VFs of E. coli genomes available through the National Antimicrobial Resistance Monitoring System GenomeTrackr database. Our objective was to determine the genetic relatedness of chicken production isolates and human clinical isolates. To achieve this aim, we first developed a massively parallel analytical pipeline (Reads2Resistome) to accurately characterize the resistome of each E. coli genome, including the AMR genes and VFs harbored. We used random forests and hierarchical clustering to show that AMR genes and VFs are sufficient to classify isolates into different pathogenic phylogroups and host origin. We found that the presence of key type III secretion system and AMR genes differentiated human clinical isolates from chicken production isolates. These results further improve our understanding of the interconnected role AMR genes and VFs play in shaping the evolution of pathogenic E. coli strains.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils. Five virus isolates, Tunturi 1–5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63–98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils. This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus

Single-cell transcriptome analysis has been extensively applied in humans and animal models to uncover gene expression heterogeneity between the different cell types of a tissue or an organ. It demonstrated its capability to discover key regulatory elements that determine cell fate during developmental programs. Single-cell analysis requires the isolation and labeling of the messenger RNA (mRNA) derived from each cell. These challenges were primarily addressed in mammals by developing microfluidic-based approaches. For plant species whose cells contain cell walls, these approaches have generally required the generation of isolated protoplasts. Many plant tissues’ secondary cell wall hinders enzymatic digestion required for individual protoplast isolation, resulting in an unequal representation of cell types in a protoplast population. This limitation is especially critical for cell types located in the inner layers of a tissue or the inner tissues of an organ. Consequently, single-cell RNA sequencing (scRNA-seq) studies using microfluidic approaches in plants have mainly been restricted to Arabidopsis roots, for which well-established procedures of protoplast isolation are available. Here we present a simple alternative approach to generating high-quality protoplasts from plant tissue by characterizing the mRNA extracted from individual nuclei instead of whole cells. We developed the protocol using two different plant materials with varying cellular complexity levels and cell wall structure, Populus shoot apices, and more lignified stems. Using the 10× Genomics Chromium technology, we show that this procedure results in intact mRNA isolation and limited leakage, with a broad representation of individual cell transcriptomes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Comparative Virulence and Genomic Analysis of Streptococcus suis Isolates

Streptococcus suis is a zoonotic bacterial swine pathogen causing substantial economic and health burdens to the pork industry. Mechanisms used by S. suis to colonize and cause disease remain unknown and vaccines and/or intervention strategies currently do not exist. Studies addressing virulence mechanisms used by S. suis have been complicated because different isolates can cause a spectrum of disease outcomes ranging from lethal systemic disease to asymptomatic carriage. The objectives of this study were to evaluate the virulence capacity of nine United States S. suis isolates following intranasal challenge in swine and then perform comparative genomic analyses to identify genomic attributes associated with swine-virulent phenotypes. No correlation was found between the capacity to cause disease in swine and the functional characteristics of genome size, serotype, sequence type (ST), or in vitro virulence-associated phenotypes. A search for orthologs found in highly virulent isolates and not found in non-virulent isolates revealed numerous predicted protein coding sequences specific to each category. While none of these predicted protein coding sequences have been previously characterized as potential virulence factors, this analysis does provide a reliable one-to-one assignment of specific genes of interest that could prove useful in future allelic replacement and/or functional genomic studies. Collectively, this report provides a framework for future allelic replacement and/or functional genomic studies investigating genetic characteristics underlying the spectrum of disease outcomes caused by S. suis isolates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Avirulent Isolates of Penicillium chrysogenum to Control the Blue Mold of Apple Caused by P. expansum

Blue mold is an economically significant postharvest disease of pome fruit that is primarily caused by Penicillium expansum. To manage this disease and sustain product quality, novel decay intervention strategies are needed that also maintain long-term efficacy. Biocontrol organisms and natural products are promising tools for managing postharvest diseases. Here, two Penicillium chrysogenum isolates, 404 and 413, were investigated as potential biocontrol agents against P. expansum in apple. Notably, 404 and 413 were non-pathogenic in apple, yet they grew vigorously in vitro when compared to the highly aggressive P. expansum R19 and Pe21 isolates. Whole-genome sequencing and species-specific barcoding identified both strains as P. chrysogenum. Each P. chrysogenum strain was inoculated in apple with the subsequent co-inoculation of R19 or Pe21 simultaneously, 3, or 7 days after prior inoculation with 404 or 413. The co-inoculation of these isolates showed reduced decay incidence and severity, with the most significant reduction from the longer establishment of P. chrysogenum. In vitro growth showed no antagonism between species, further suggesting competitive niche colonization as the mode of action for decay reduction. Both P. chrysogenum isolates had incomplete patulin gene clusters but tolerated patulin treatment. Finally, hygromycin resistance was observed for both P. chrysogenum isolates, yet they are not multiresistant to apple postharvest fungicides. Overall, we demonstrate the translative potential of P. chrysogenum to serve as an effective biocontrol agent against blue mold decay in apples, pending practical optimization and formulation.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1975

Positive isolation disconnect

A positive isolation disconnect was developed for component replacement in serviced liquid and gaseous spacecraft systems. Initially a survey of feasible concepts was made to determine the optimum method for fluid isolation, sealing techniques, coupling concepts, and foolproofing techniques. The top concepts were then further evaluated, including the fabrication of a semifunctional model. After all tradeoff analyses were made, a final configuration was designed and fabricated for development testing. This resulted in a 6.35 mm (1/4 inch) line and 12.7 mm (1/2 inch) line positive isolation disconnect, each unit consisting of two coupled disconnect halves, each capable of fluid isolation with essentially zero clearance between them for zero leakage upon disconnect half disengagement. An interlocking foolproofing technique was incorporated that prevents uncoupling of disconnect halves prior to fluid isolation.

Rosener, A. A.↗

NASA NTRS1976

Status of 30-centimeter-diameter mercury ion thruster isolator development

Results are presented of several 30 cm diameter mercury ion thruster isolator life tests that show that the onset and exponential increase of leakage current problems observed in earlier thruster operations and isolator tests have been solved. A 10,006 hour life test of a main isolator vaporizer operated with no mercury flow at 320 C and 1500 volts was found to have no onset of leakage current during the test. A cathode-isolator vaporizer operated with a mercury discharge at 340 to 360 C and 1200 volts for 18,000 hours, was found to have a small increase of leakage current with time. A 10,000 hour thruster life test exhibited no increase of leakage current during the life test. Isolators have been developed which will satisfy 30 cm mercury ion thruster mission requirements.

Mantenieks, M. A.↗

NASA NTRS1976

Status of 30-centimeter-diameter mercury ion thruster isolator development

Results are presented for several 30-cm-diameter mercury-ion-thruster isolator life tests which show that the onset and exponential increase of leakage-current problems observed in earlier thruster operations and isolator tests have been solved. A 10,006-hour life test of a main isolator-vaporizer operated with no mercury flow at 320 C and 1500 volts was found to have no onset of leakage current during the test. A cathode-isolator-vaporizer (CIV) operated with a mercury discharge at 340 to 360 C and 1200 volts for 18,000 hours was found to have a small increase (0.004 micro A/hr) in leakage current with time. A 10,000-hour thruster life test exhibited no increase in leakage current during the life test. It is concluded that isolators have been developed which will satisfy 30-cm mercury-ion-thruster mission requirements.

Mantenieks, M. A.↗

NASA NTRS1989

Nonintrusive inertial vibration isolation technology for microgravity space experiments

The dynamic acceleration environment observed on Space Shuttle flights to date and predicted for the Space Station has complicated the analysis of prior microgravity experiments and prompted concern for the viability of proposed space experiments requiring long-term, microgravity environments. Isolation systems capable of providing significant improvements to this environment exist, but at present have not been demonstrated in flight configurations. A summary of the theoretical evaluation for two one degree-of-freedom (DOF) active magnetic isolators and their predicted response to both direct and base excitations is presented. These isolators can be used independently or in concert to isolate acceleration-sensitive microgravity space experiments, dependent on the isolation capability required for specific experimenter needs.

Grodsinsky, Carlos M.↗

NASA NTRS1990

Nonintrusive inertial vibration isolation technology for microgravity space experiments

Grodsinsky, Carlos M.↗

NASA NTRS1990

Development of a vibration isolation prototype system for microgravity space experiments

The presence of small levels of low-frequency accelerations on the space shuttle orbiters has degraded the microgravity environment for the science community. Growing concern about this microgravity environment has generated interest in systems that can isolate microgravity science experiments from vibrations. This interest has resulted primarily in studies of isolation systems with active methods of compensation. The development of a magnetically suspended, six-degree-of-freedom active vibration isolation prototype system capable of providing the needed compensation to the orbital environment is presented. A design for the magnetic actuators is described, and the control law for the prototype system that gives a nonintrusive inertial isolation response to the system is also described. Relative and inertial sensors are used to provide an inertial reference for isolating the payload.

Logsdon, Kirk A.↗

NASA NTRS1991

Development of a vibration isolation prototype system for microgravity space experiments

The presence of small levels of low-frequency accelerations on the Space Shuttle orbiters has degraded the microgravity environment for the science community. Growing concern about this microgravity environment has generated interest in systems that can isolate microgravity science experiments from vibrations. This interest has resulted primarily in studies of isolation systems with active methods of compensation. The development of a magnetically suspended, six-degree-of-freedom active vibration isolation prototype system capable of providing the needed compensation to the orbital environment is presented. A design for the magnetic actuators is described, and the control law for the prototype system that gives a nonintrusive inertial isolation respone to the system is also described. Relative and inertial sensors are used to provide an inertial reference for isolating the payload.

Logsdon, K. A.↗