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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Data for Metabolic Engineering of Rhodotorula toruloides IFO0880 Improves C16 and C18 Fatty Alcohol Production from Synthetic Media

The oleaginous, carotenogenic yeast Rhodotorula toruloides has been increasingly explored as a platform organism for the production of terpenoids and fatty acid derivatives. Fatty alcohols, a fatty acid derivative widely used in the production of detergents and surfactants, can be produced microbially with the expression of a heterologous fatty acyl-CoA reductase. Due to its high lipid production, R. toruloides has high potential for fatty alcohol production, and in this study several metabolic engineering approaches were investigated to improve the titer of this product. Fatty acyl-CoA reductase from Marinobacter aqueolei was co-expressed with SpCas9 in R. toruloides IFO0880 and a panel of gene overexpressions and Cas9-mediated gene deletions were explored to increase the fatty alcohol production. Two overexpression targets (ACL1 and ACC1, improving cytosolic acetyl-CoA and malonyl-CoA production, respectively) and two deletion targets (the acyltransferases DGA1 and LRO1) resulted in significant (1.8 to 4.4-fold) increases to the fatty alcohol titer in culture tubes. Combinatorial exploration of these modifications in bioreactor fermentation culminated in a 3.7 g/L fatty alcohol titer in the LRO1Δ mutant. As LRO1 deletion was not found to be beneficial for fatty alcohol production in other yeasts, a lipidomic comparison of the DGA1 and LRO1 knockout mutants was performed, finding that DGA1 is the primary acyltransferase responsible for triacylglyceride production in R. toruloides , while LRO1 disruption simultaneously improved fatty alcohol production, increased diacylglyceride and triacylglyceride production, and increased glucose consumption. The fatty alcohol titer of fatty acyl-CoA reductase-expressing R. toruloides was significantly improved through the deletion of LRO1, or the deletion of DGA1 combined with overexpression of ACC1 and ACL1. Disruption of LRO1 surprisingly increased both lipid and fatty alcohol production, creating a possible avenue for future study of the lipid metabolism of this yeast.

Conversion↗
DOE OSTI2026

Data for Mitochondrial ATP Generation is More Proteome Efficient than Glycolysis

Metabolic efficiency profoundly influences organismal fitness. Heterotrophs, from yeast to mammals, derive usable energy primarily through glycolysis and respiration. While respiration is more energy-efficient, some cells favor glycolysis even when oxygen is available (aerobic glycolysis, Warburg effect). A leading explanation is that glycolysis is more efficient in terms of ATP production per unit mass of protein (i.e. faster). Through quantitative flux analysis and proteomics, we find however that mitochondrial respiration is actually more proteome-efficient than aerobic glycolysis. This is shown across yeasts, T cells, cancer cells, and tissues and tumors in vivo. Instead of aerobic glycolysis being valuable for fast ATP production, it correlates with high glycolytic protein expression, which is valuable for hypoxic growth. Aerobic glycolytic yeasts do not excel at aerobic growth, but outgrow respiratory cells in oxygen limitation. Thus, aerobic glycolysis emerges from cells maintaining a proteome conducive to both aerobic and hypoxic growth.

Metabolomics↗
DOE OSTI2023

Dissecting the Division of Labor in Microbial Consortia for the Production of Biofuels and Chemicals (Final Technical Report)

The overarching objective of this project is to elucidate the fundamental design rules for microbial division of labor (DOL), the core of ecosystem organization, in the context of artificial yeast—lactic acid bacteria consortia that produce advanced biofuel and chemical from cellulosic biomass. Over the course of four years, we have successfully achieved the objective through three lines of research that combines experiment with mathematical modeling. Specifically, we have shown that compositional and temporal DOL is effective in modulating mixed sugar fermentation by an engineered consortium and uncovered general quantitative criteria for conditions under which microbial DOL outperforms single superbugs for simultaneous utilization of mixed substrates. We also demonstrated, in synthetic consortia of yeast and lactic acid bacteria, that partitioning the labor for substrate breakdown and end-product synthesis can allow an efficient production of 2-butanol that is difficult otherwise for a single yeast strain. Additionally, by systematically probing the stability of an engineered cooperative consortium, we found that the stability of microbial symbiosis is governed by the topological structure of the underlying cellular interactions rather than specific microbial species and that rational modulation of the interactions may facilitate the restoration of collapsed consortia as well as the intervention of target communities. Together, this project has advanced the fundamental knowledge of microbial DOL in terms of its strength in mixed substrate fermentation, production of complex chemicals, and ecological system stability in the context of microbial consortia. It also provides valuable insights into the design, construction and optimization of artificial consortia for the utilization of cellulosic biomass and economic production of biofuel and chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Enhancing organic matter removal, product recovery, and hydrogen generation from fermentation wastewater

Existing ethanol biorefineries produce billions of gallons of wastewater (stillage) that must be treated extensively prior to discharge or concentrated in an energy intense evaporation step to produce animal feed as a value-added bioproduct. Yeasts and filamentous fungi were screened for growth and reduction of soluble organic compounds, carbohydrates, and protein from stillage to identify species capable of rapidly concentrating organic compounds into readily separable biomass in an attempt to concentrate the product using a much more efficient centrifugation step. Yeasts amenable to production of biomass derived products including bio-oils (Yarrowia lipolytica and Rhodotorula pallida), chitosan (Aspergillus niger) and animal feed (Cyberlindnera jadinii) were identified as well as microbes capable of efficient production of small organic acids with applications as bioderived polymers including 3-hydroxypropionic acid (engineered A. niger) and lactic acid using a co-culture of Debaryomyces udenii and Lactobacillus pentosus. The filamentous fungus A. niger eliminated all specifically measured soluble organics (glycerol, acetate, lactate, ethanol, and citrate) in under 48 hours and reduced total soluble protein content by 46% and total carbohydrate content by 83% within 96 hours, the greatest reduction in organic content observed. During this process an A. niger strain engineered to produce 3-hydroxypropionic acid achieved a yield of 0.35 C-mol 3HP / C-mol non-protein organics consumed at an overall rate of 0.09 g/Lh in unmodified stillage without pH control. Stillage treated by the fodder yeast C. jadinii as well as stillage containing acetic or lactic acid was found to be most suitable for growth by electrogenic bacteria with applications in production of electricity or hydrogen from wastewater. This work establishes fungal and bacterial strains appropriate for biological treatment of stillage to produce biomass derived products, soluble commodity chemicals, energy, and treated water to reduce the energy intensity and improve the economics of ethanol biorefineries.

09 BIOMASS FUELS↗
DOE OSTI2020

Creating multifunctional synthetic lichen platforms for sustainable biosynthesis of biofuel precursors

In this project, we were creating a sustainable platform for biofuel production, utilizing carbon-fixing autotrophs to supply oxygen and organic substrates to heterotrophic partners, which in turn produce carbon dioxide to feed the autotrophs. This symbiotic lichen community could lower the input cost, optimize metabolic exchanges and improve the generation of biofuel precursors through multi-omics driven genetic engineering. The cyanobacteria Synechococcus elongatus (S. elongatus) was used as the primary autotroph to provide oxygen and organic substrates, especially sucrose, to a co-culture system. The strain with overexpression of sucrose transporter cscB demonstrated a significant increase in sucrose production under salt stress as what we expected. We also implemented 13C metabolic flux analysis on the sucrose secreting strain S. elongatus cscB-NaCl. Next, transporters proteins like glutamate exporter mscCG from Corynebacterium glutamicum was overexpressed in S. elongatus to improve metabolite exchange. We provided sucrose and glutamate to filamentous fungi to enable their growth and production of biochemicals using substrates from the cyanobacterium. Two fungi ( Aspergillus nidulans and Aspergillus niger ) and two yeast strains ( Rhodotorula toruloides and Lipomyces starkeyi ) served as heterotrophs in this system. They were co-cultured with S.elongatus under different pH condition, and growth on different carbon source to understand the symbiotic system and optimize the parameters for production. The two fungi strained grew much better at pH 7, 8 and 9 with Yeast Nitrogen Base (YNB ) supplementation. Two yeast strains grew well on pH 7 and 8 with YNB supplementation. All four species achieved the highest biomass level when utilizing sucrose as the main carbon sources, which demonstrates a great pairing with S.elongatus . In addition to investigate the metabolite exchange and growth condition of the co-culture system, we incorporated an Aspergillus strain expressing three genes (PAND, BAPAT and HPDH). Expression of these three genes enabled production of 3-hydroxypropionic acid (3HP) with a titer of 3-6 g/L regardless of pH and other nutrient conditions. Moreover, we developed a computational model with different heterotrophic fungi symbiosing with S.elongatus to evaluate the exchange of hundreds of metabolites. The accuracy and sensitivity had been optimized by high-throughput phenotyping assays. This project demonstrated ways to enhance a synthetic lichen platform’s efficiency and scalability to create a robust system for sustainable bioproduct synthesis. The project has enabled us to explore the technological and commercial potential of sustainable lichen co-culture. The project has also trained the next generation of scientists to address sustainability, carbon fixation, and design solutions to contemporary global challenges. The lichen platform represented a novel approach to sustainably producing bioproducts with a reduced carbon footprint and lower costs.

09 BIOMASS FUELS↗
DOE OSTI2023

The Interaction between the DOCK7 Protein and the E2 Protein of Classical Swine Fever Virus Is Not Involved with Viral Replication or Pathogenicity

The classical swine fever virus (CSFV) particle consists of three glycoproteins, all of which have been shown to be important proteins involved in many virus functions, including interaction with several host proteins. One of these proteins, E2, has been shown to be directly involved with adsorption to the host cell and important for virus virulence. Using the yeast two-hybrid system, we have previously shown that CSFV E2 specifically interacts with the (DOCK7) dedicator of cytokinesis, a scaffolding protein. In this report, the interaction between E2 and DOCK7 was evaluated. To confirm the yeast two-hybrid results and to determine that DOCK7 interacts in swine cells with E2, we performed co-immunoprecipitation and proximity ligation assay (PLA). After demonstrating the protein interaction in swine cells, E2 amino acid residues Y65, V283, and T149 were determined to be critical for interaction with Dock7 by using a random mutated library of E2 and a reverse yeast two-hybrid approach. That disruption of these three residues with mutations Y65F, V283D, and T149A abrogated the Dock7-E2 protein interaction. These mutations were then introduced into a recombinant CSFV, E2DOCK7v, by a reverse genomics approach using the highly virulent CSFV Brescia isolate as a backbone. E2DOCKv was shown to have similar growth kinetics in swine primary macrophages and SK6 cell cultures to the parental Brescia strain. Similarly, E2DOCK7v demonstrated a similar level of virulence to the parental Brescia when inoculated in domestic pigs. Animals intranasally inoculated with 10 5 TCID 50 developed a lethal form of clinical disease with virological and hematological kinetics changes indistinguishable from that produced by the parental strain. Therefore, interaction between CSFV E2 and host DOCK7 is not critically involved in the process of virus replication and disease production.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Therapeutic genetic variation revealed in diverse Hsp104 homologs

The AAA+ protein disaggregase, Hsp104, increases fitness under stress by reversing stress-induced protein aggregation. Natural Hsp104 variants might exist with enhanced, selective activity against neurodegenerative disease substrates. However, natural Hsp104 variation remains largely unexplored. Here, we screened a cross-kingdom collection of Hsp104 homologs in yeast proteotoxicity models. Prokaryotic ClpG reduced TDP-43, FUS, and α-synuclein toxicity, whereas prokaryotic ClpB and hyperactive variants were ineffective. Furthermore, we uncovered therapeutic genetic variation among eukaryotic Hsp104 homologs that specifically antagonized TDP-43 condensation and toxicity in yeast and TDP-43 aggregation in human cells. We also uncovered distinct eukaryotic Hsp104 homologs that selectively antagonized α-synuclein condensation and toxicity in yeast and dopaminergic neurodegeneration in C. elegans . Surprisingly, this therapeutic variation did not manifest as enhanced disaggregase activity, but rather as increased passive inhibition of aggregation of specific substrates. By exploring natural tuning of this passive Hsp104 activity, we elucidated enhanced, substrate-specific agents that counter proteotoxicity underlying neurodegeneration.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1979

Effects of aeration on formation and localization of the acetyl coenzyme A synthetases of Saccharomyces cerevisiae

Previous studies on the yeast Saccharomyces cerevisiae have shown that two different forms of the enzyme acetyl coenzyme A synthetase (ACS) are present, depending on the conditions under which the cells are grown. The paper evaluates the usefulness of a method designed to assay both synthetases simultaneously in yeast homogenates. The data presented confirm the possibility of simultaneous detection and estimation of the amount of both ACSs of S. cerevisiae in crude homogenates of this strain, making possible the study of physiological factors involved in the formation of these isoenzymes. One important factor for specifying which of the two enzymes is found in these yeast cells is the presence or absence of oxygen in their environment. Aeration not only affects the ratio of the two ACSs but also appears to affect the cellular distribution of these enzymes. Most of the data presented suggest the possibility that the nonaerobic ACS may serve as a precursor to the aerobic form.

Klein, H. P.↗
NASA NTRS1988

Reproducible analyses of microbial food for advanced life support systems

The use of yeasts in controlled ecological life support systems (CELSS) for microbial food regeneration in space required the accurate and reproducible analysis of intracellular carbohydrate and protein levels. The reproducible analysis of glycogen was a key element in estimating overall content of edibles in candidate yeast strains. Typical analytical methods for estimating glycogen in Saccharomyces were not found to be entirely aplicable to other candidate strains. Rigorous cell lysis coupled with acid/base fractionation followed by specific enzymatic glycogen analyses were required to obtain accurate results in two strains of Candida. A profile of edible fractions of these strains was then determined. The suitability of yeasts as food sources in CELSS food production processes is discussed.

Petersen, Gene R.↗
NASA NTRS2003

Design Study Conducted of a Stirred and Perfused Specimen Chamber for Culturing Suspended Cells on the International Space Station

A tightly knit numerical/experimental collaboration among the NASA Ames Research Center, NASA Glenn Research Center, and Payload Systems, Inc., was formed to analyze cell culturing systems for the International Space Station. The Cell Culture Unit is a facility scheduled for deployment on the space station by the Cell Culture Unit team at Ames. The facility houses multiple cell specimen chambers (CSCs), all of which have inlets and outlets to allow for replenishment of nutrients and for waste removal. For improved uniformity of nutrient and waste concentrations, each chamber has a pair of counterrotating stir bars as well. Although the CSC can be used to grow a wide variety of organic cells, the current study uses yeast as a model cell. Previous work identified groundbased protocols for perfusion and stirring to achieve yeast growth within the CSC that is comparable to that for yeast cultures grown in a shaken Ehrlenmeyer flask.

Nelson, Emily S.↗
NASA NTRS2017

EcAMSat and BioSentinel: Autonomous Bio Nanosatellites Addressing Strategic Knowledge Gaps for Manned Spaceflight Beyond LEO

Manned missions beyond low Earth orbit (LEO) require that several strategic knowledge gaps about the effects of space travel on the human body be addressed. NASA Ames Research Center has been the leader in developing autonomous bio nanosatellites, including past successful missions for GeneSat, PharmaSat, and O/OREOS, that tackled some of these issues. These nanosatellites provide in situ measurements, which deliver insight into the dynamic changes in cell behavior in microgravity. In this talk, two upcoming bio nanosatellites developed at Ames, the E. coli Antimicrobial Satellite (EcAMSat) and BioSentinel, will be discussed. Both satellites contain microfluidic systems that precisely deliver nutrients to the microorganisms stored within wells of fluidic cards. Each well, in turn, has its own 3-color LED and detector system which is used to monitor changes in metabolic activity with alamarBlue, a redox indicator, and the optical density of the cells. EcAMSat investigates the effects of microgravity on bacterial resistance to antimicrobial drugs, vital knowledge for understanding how to maintain the health of astronauts in long-term and beyond LEO spaceflight. The behavior of wild type and mutant uropathic E. coli will be compared in microgravity and with ground data to help understand the molecular mechanisms behind antibiotic resistance and how these phenotypes might change in space. BioSentinel seeks to directly measure the effects of space radiation on budding yeast S. cerevisiae, particularly double strand breaks (DSB). While hitching a ride on the SLS EM-1 mission (Orion's first unmanned mission to the moon) in 2018, BioSentinel will be kicked off and enter into a heliocentric orbit, becoming the first study of the effects of radiation on living organisms outside LEO since the Apollo program. The yeast are stored in eighteen independent 16-well microfluidic cards, which will be individually activated over the 12 month mission duration. In addition to the wild type and radiation-sensitive mutant strains, a BioSentinel strain of yeast has been developed, which requires a DSB to reactivate growth, thereby allowing for a direct measurement of DSBs caused by radiation. These two missions demonstrate the utility of using autonomous nanosatellites to address strategic knowledge gaps in the push to once again extend manned spaceflight beyond LEO.

Padgen, Michael R.↗
NASA NTRS2017

EcAMSat and BioSentinel: Autonomous Bio Nanosatellites Addressing Strategic Knowledge Gaps for Manned Spaceflight Beyond LEO

Manned missions beyond low Earth orbit (LEO) require that several strategic knowledge gaps about the effects of space travel on the human body be addressed. NASA Ames Research Center has been the leader in developing autonomous bio nanosatellites, including past successful missions for GeneSat, PharmaSat, and OOREOS, that tackled some of these issues. These nanosatellites provide in situ measurements, which deliver insight into the dynamic changes in cell behavior in microgravity. In this talk, two upcoming bio nanosatellites developed at Ames, the E. coli Antimicrobial Satellite (EcAMSat) and BioSentinel, will be discussed. Both satellites contain microfluidic systems that precisely deliver nutrients to the microorganisms stored within wells of fluidic cards. Each well, in turn, has its own 3-color LED and detector system which is used to monitor changes in metabolic activity with alamarBlue, a redox indicator, and the optical density of the cells. EcAMSat investigates the effects of microgravity on bacterial resistance to antimicrobial drugs, vital knowledge for understanding how to maintain the health of astronauts in long-term and beyond LEO spaceflight. The behavior of wild type and mutant uropathic E. coli will be compared in microgravity and with ground data to help understand the molecular mechanisms behind antibiotic resistance and how these phenotypes might change in space. BioSentinel seeks to directly measure the effects of space radiation on budding yeast S. cerevisiae, particularly double strand breaks (DSB). While hitching a ride on the SLS EM-1 mission (Orions first unmanned mission to the moon) in 2018, BioSentinel will be kicked off and enter into a heliocentric orbit, becoming the first study of the effects of radiation on living organisms outside LEO since the Apollo program. The yeast are stored in eighteen independent 16-well microfluidic cards, which will be individually activated over the 12 month mission duration. In addition to the wild type and radiation-sensitive mutant strains, a BioSentinel strain of yeast has been developed, which requires a DSB to reactivate growth, thereby allowing for a direct measurement of DSBs caused by radiation. These two missions demonstrate the utility of using autonomous nanosatellites to address strategic knowledge gaps in the push to once again extend manned spaceflight beyond LEO.

Padgen, Mike↗
NASA NTRS2017

Identification of Novel Desiccation-Tolerant S. cerevisiae Strains for Deep Space Biosensors

NASA's BioSentinel mission, a secondary payload that will fly on the Space Launch System's first Exploration Mission (EM-1), utilizes the budding yeast S. cerevisiae to study the biological response to the deep space radiation environment. Yeast samples are desiccated prior to launch to suspend growth and metabolism while the spacecraft travels to its target heliocentric orbit beyond Low Earth Orbit. Each sample is then rehydrated at the desired time points to reactivate the cells. A major risk in this mission is the loss of cell viability that occurs in the recovery period following the desiccation and rehydration process. Cell survival is essential for the detection of the biological response to features in the deep space environment, including ionizing radiation. The aim of this study is to mitigate viable cell loss in future biosensors by identifying mutations and genes that confer tolerance to desiccation stress in rad51, a radiation-sensitive yeast strain. We initiated a screen for desiccation-tolerance after rehydrating cells that were desiccated for three years, and selected various clones exhibiting robust growth. To verify retention of radiation sensitivity in the isolated clones - a crucial feature for a successful biosensor - we exposed them to ionizing radiation. Finally, to elucidate the genetic and molecular bases for observed desiccation-tolerance, we will perform whole-genome sequencing of those rad51 clones that exhibit both robust growth and radiation sensitivity following desiccation. The identification and characterization of desiccation-tolerant strains will allow us to engineer a biological model that will be resilient in face of the challenges of the deep space environment, and will thus ensure the experimental success of future biosensor missions.

S. cerevisiae↗
NASA NTRS2017

Identification of Novel Desiccation-Tolerant S. cerevisiae Strains for Deep Space Biosensors

NASA's BioSentinel mission, a secondary payload that will fly on the Space Launch Systems first Exploration Mission (EM-1), utilizes the budding yeast S. cerevisiae to study the biological response to the deep space radiation environment. Yeast samples are desiccated prior to launch to suspend growth and metabolism while the spacecraft travels to its target heliocentric orbit beyond Low Earth Orbit. Each sample is then rehydrated at the desired time points to reactivate the cells. A major risk in this mission is the loss of cell viability that occurs in the recovery period following the desiccation and rehydration process. Cell survival is essential for the detection of the biological response to features in the deep space environment, including ionizing radiation.The aim of this study is to mitigate viable cell loss in future biosensors by identifying mutations and genes that confer tolerance to desiccation stress in rad51, a radiation-sensitive yeast strain. We initiated a screen for desiccation-tolerance after rehydrating cells that were desiccated for three years, and selected various clones exhibiting robust growth. To verify retention of radiation sensitivity in the isolated clonesa crucial feature for a successful biosensorwe exposed them to ionizing radiation. Finally, to elucidate the genetic and molecular bases for observed desiccation-tolerance, we will perform whole-genome sequencing of those rad51 clones that exhibit both robust growth and radiation sensitivity following desiccation. The identification and characterization of desiccation-tolerant strains will allow us to engineer a biological model that will be resilient in face of the challenges of the deep space environment, and will thus ensure the experimental success of future biosensor missions.

S. cerevisiae↗
NASA NTRS2023

A Multi-Sensor, Low Volume, Automated Culture System for Space Biology Experiments

Optical density (absorbance) is commonly used in microbiology to measure cell concentration and other colorimetric indicators. It is the main type of bioscience data returned from the BioSentinel small spacecraft mission, which was recently launched as a secondary payload on Artemis I. The flight unit takes absorbance measurements of yeast cultures at 570 nm, 630 nm, and 850 nm to track cell concentration and oxidation-reduction (redox) state of the metabolic indicator dye alamarBlue over time [1]. Because the data returned from a small spacecraft mission is necessarily limited, BioSentinel uses a specialized ground-based experiment apparatus to map the absorbance data onto several other parameters. This culture apparatus is composed of a polycarbonate base and lid which contain ports for several commercial sensors, including a standard 12 mm dissolved oxygen probe, gaseous CO2, fluid pressure, and two micro-probes for measuring pH and redox potential. It also contains a pressure relief valve, a rubber membrane for culture interaction, and a 12mm port for the custom optical probe designed to match in-flight measurements. Modules in two corners expand the culture volume into narrow columns, enabling solid-state optical density measurement and dielectric spectroscopy. The apparatus can be fit to a plate for magnetic stirring. The apparatus’s optical probe allows mapping between the flight unit’s optical data and the additional parameters measured by the ground-based experiments. Within the probe, a linear actuator pulls a plunger, drawing culture volume into the optical path. The actuator then pushes out the plunger and culture volume, cleaning any stray yeast from the inside surface of the probe. The probe chassis is 3D-printed from biocompatible resin with the optoelectronics cured inside an optically clear conformal coat which functions as a lens. To optimize the probe’s dimensions, including optical path, a test harness was developed to manipulate and measure distance while the LED light sources and photodiode detector are in operation. The test harness was composed of two 3/64” thick polycarbonate plates mounted to a set of calipers. The LEDs and photodiode were mounted on the outside of each plate. A cuvette of sample fluid was then clamped between the plates in line between the LEDs and photodiode. The test harness generated a 78% signal change between water and a dye standard for the green (570 nm) LED, a 90% signal change for the red (630 nm) LED, and a 25% signal change between water and overgrown yeast for the infrared (850 nm) LED. The improvements to the ground experiment apparatus (culture volume reduction, inclusion of an optical probe to measure flight-like optical data, and magnetic stirring for culture homogeneity) allow for more flight-like measurements to be taken and more accurate mapping of these additional parameters to the optical data returned from the flight unit. This enhancement to mission science return will give insight into how deep space radiation may affect human biology for future long-term space exploration.

Multi-Sensor↗
DOE OSTI2020

Metal Bioavailability and Ecotoxicity of Bioremediated Oils and Tailings by BioTiger{sup TM}, a Microbial Consortium

Oil Sands and Mature Fine Tailings: Oil sand reserves are a major source of oil for the United States. Oil sands are a mixture of sand, clay, water, and bitumen. The refining process requires large volumes of water and generates hazardous Mature Fine Tailings (MFTs) that are stored in engineered settling ponds. They are of major environmental concern due to their persistence and difficulty to naturally biodegrade. MFT Contaminants of Concern: Naphthenic Acids (NAs), Polycyclic Aromatic Hydrocarbons (PAHs), Benzene, Toluene, Ethylbenzene and Xylene (BTEX), Metals, Residual Bitumen. BioTiger{sup TM} (BT{sup TM}), the SRNL patented 12 component microbial consortia was found to cometabolically degrade some NAs and PAHs. Previous studies performing short term exposure (48 hours and 7 days) to BT{sup TM} have resulted in increased toxicity due to the partial degradation of PAHs forming toxic intermediates. Objective: Evaluate the ecotoxicity of BT{sup TM} remediated MFTs exposed to a 2 week period w/ yeast (Y) extract. This work will determine BT{sup TM}'s remediation of MFTs from Fort McMurray, Alberta. Acute toxicity tests will be performed under section 9 of EPA's Method for Measuring Acute Toxicity using the freshwater organism, Ceriodaphnia dubia. Monitor BT{sup TM} growth through Most Probable Number (MPN) counts, pH, and metal bioavailability will also be evaluated. Preparing tailing solutions for biodegradation: BT{sup TM} components were grown in R2A media and combined. Mother BT{sup TM} was centrifuged at 7000 rpm for 20 minutes and resuspended in Bushnell Haus. 33 g of tailings were added to 1100 mL Bushnell Haus along with yeast extract (11 g) to create a 3% tailing solution. Treatments were performed in triplicate. Preparing solutions for toxicity tests using C. dubia: Supernatant was collected immediately after centrifuging at 7000 rpm for 20 min. Supernatant was filtered via a 0.22 μm sterile system. All treatments except MFT, Y peaked at T=4. This decrease in microbial growth could be associated with toxicity from intermediate byproducts. Treatments containing only MFTs decreased in the initial 11 days before growing significantly. Final solution for MFT, Y treatment had the highest pH. This could potentially be due to increased microbial activity linked with yeast consumption. All treatments except MFT, Y peaked at T=4. This decrease in microbial growth could be associated with toxicity from intermediate byproducts. Treatments containing only MFTs decreased in the initial 11 days before growing significantly. Future Direction: Await results from Acute Toxicity Tests and Metal Bioavailability Quantification of biosurfactant production. Evaluate hydrocarbon degradation byproducts using an analytical chemistry approach. More toxicity experiments with variations in time and conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae . A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S . cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S . cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum . Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae . The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S . cerevisiae .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Scaled-up fabrication of durable and porous adsorbent-coated minichannels on aluminum for CO 2 separation

A method was developed to fabricate zeolite 13X adsorbent-coated minichannels on aluminum for CO₂ adsorption applications in this study. It emphasizes the innovative use of aluminum as a substrate, which offers airtight assembly, paving the way for highly efficient adsorption systems. An optimized coating process was developed using a slurry of Zeolite 13X, yeast, sugar, and xanthan gum, resulting in durable and highly porous layers that enhance CO₂ capture performance. A PETG peeler was designed to remove the top layer of the yeast-engineered adsorbent coatings, revealing a super porous and foamy structure. The teeth of the peeler were designed and fabricated for high repeatability and rapid prototyping. Breakthrough experiments were conducted on the scaled-up adsorbent bed using gas mixtures of 80% CO₂, 20% N₂, and 20% CO₂, 80% N₂ to represent different industrial scenarios. The performance of the bed was evaluated at flow rates of 160 and 190 cm³ min -1 using a Raman Laser Gas Analyzer (RLGA), demonstrating stable adsorption without degradation across multiple cycles. Computational modeling of integral transport phenomena under the chosen experimental conditions was pursued using gPROMS ProcessBuilder™, and the modeling results were compared with those from the tests for adsorption time, which resulted in an error margin of 2% to 9% for the breakthrough time, confirming the easy reproducibility of the design through modeling. This research advances CO₂ capture technologies by providing an effective and scalable solution for producing aluminum-based adsorbent coated beds, supporting industrial carbon capture efforts.

CO2 capture↗