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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Short Chain Fatty Acids and Bacterial Taxa Associated with Reduced Salmonella enterica serovar I 4,[5],12:i:- Shedding in Swine Fed a Diet Supplemented with Resistant Potato Starch

Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen of concern because many isolates are multidrug-resistant (resistant to ≥3 antimicrobial classes) and metal tolerant. In this study, three in-feed additives were individually tested for their ability to reduce Salmonella I 4,[5],12:i:- shedding in swine: resistant potato starch (RPS), high amylose corn starch, and a fatty acid blend, compared with a standard control diet over 21 days. Only RPS-fed pigs exhibited a reduction in Salmonella fecal shedding, different bacterial community compositions, and different cecal short chain fatty acid (SCFA) profiles relative to control animals. Within the RPS treatment group, pigs shedding the least Salmonella tended to have greater cecal concentrations of butyrate, valerate, caproate, and succinate. Additionally, among RPS-fed pigs, several bacterial taxa (Prevotella_7, Olsenella, and Bifidobacterium, and others) exhibited negative relationships between their abundances of and the amount of Salmonella in the feces of their hosts. Many of these same taxa also had significant positive associations with cecal concentrations of butyrate, valerate, caproate, even though they are not known to produce these SCFAs. Together, these data suggest the RPS-associated reduction in Salmonella shedding may be dependent on the establishment of bacterial cross feeding interactions that result in the production of certain SCFAs. However, directly feeding a fatty acid mix did not replicate the effect. RPS supplementation could be an effective means to reduce multidrug-resistant (MDR) S. enterica serovar I 4,[5],12:i:- in swine, provided appropriate bacterial communities are present in the gut.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Large Pilot Scale Testing of Linde/BASF Post-Combustion CO 2 Capture Technology at the Abbott Coal-Fired Power Plant

The work summarized in this report is the first step towards a project that will re-train and create jobs for personnel in the coal industry and continue regional economic development to benefit regions impacted by previous downturns. The larger project is aimed at capturing ~300 tons/day (272 metric tonnes/day) CO 2 at a 90% capture rate from existing coal- fired boilers at the Abbott Power Plant on the campus of University of Illinois (UI). It will employ the Linde-BASF novel amine-based advanced CO 2 capture technology, which has already shown the potential to be cost-effective, energy efficient and compact at the 0.5-1.5 MWe pilot scales. The overall objective of the project is to design and install a scaled-up system of nominal 15 MWe size, integrate it with the Abbott Power Plant flue gas, steam and other utility systems, and demonstrate the viability of continuous operation under realistic conditions with high efficiency and capacity. The project will also begin to build a workforce that understands how to operate and maintain the capture plants by including students from regional community colleges and universities in the operation and evaluation of the capture system. This project will also lay the groundwork for follow-on projects that pilot utilization of the captured CO 2 from coal-fired power plants. The net impact will be to demonstrate a replicable means to (1) use a standardized procedure to evaluate power plants for their ability to be retrofitted with a pilot capture unit; (2) design and construct reliable capture systems based on the Linde-BASF technology; (3) operate and maintain these systems; (4) implement training programs with local community colleges and universities to establish a workforce to operate and maintain the systems; and (5) prepare to evaluate at the large pilot scale level various methods to utilize the resulting captured CO 2 . Towards the larger project goal, the UI-led team, together with Linde, has completed a preliminary design for the carbon capture pilot plant with basic engineering and cost estimates, established permitting needs, identified approaches to address Environmental, Health, and Safety concerns related to pilot plant installation and operation, developed approaches for long-term use of the captured carbon, and established strategies for workforce development and job creation that will re-train coal operators to operate carbon capture plants. This report describes Phase I accomplishments and demonstrates that the project team is well-prepared for full implementation of Phase 2, to design, build, and operate the carbon capture pilot plant.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2019

Resilience Roadmap: A Collaborative Approach to Multi-Jurisdictional Resilience Planning

Extreme weather and aging infrastructure are creating unprecedented challenges in the United States and around the globe. Many communities have suffered damages from a variety of weather-related events, such as severe weather such as hurricanes, droughts, increasing temperatures, wildfires, and storm surges. Numerous efforts exist to improve resilience to protect national security, energy and water security, economic well-being, and quality of life. As severe weather events increase in frequency and severity, many cities, states, tribes, and federal agencies are addressing the impacts through resilience planning and measures. In an effort to support communities with resilience planning, the White House Council on Environmental Quality (CEQ) initiated preparedness pilot projects designed to showcase community resilience planning in the City of Houston and the State of Colorado. This publication is the full, technical document, for the Colorado pilot project. The process is also summarized in a user-friendly web-version on NREL's website (visit www.nrel.gov/resilience-planning-roadmap) for easier access and replicability. NASA's pilot project with the City of Houston is summarized separately (visit https://toolkit.climate.gov/case-studies/climate-resilience to learn more). water security, economic well-being, and quality of life. As severe weather events increase in frequency and severity, many cities, states, tribes, and federal agencies are addressing the impacts through resilience planning and measures. In an effort to support communities with resilience planning, the White House Council on Environmental Quality (CEQ) initiated preparedness pilot projects designed to showcase community resilience planning in the City of Houston and the State of Colorado. This publication is the full, technical document, for the Colorado pilot project. The process is also summarized in a user-friendly web-version on NREL's website (visit www.nrel.gov/resilience-planning-roadmap) for easier access and replicability. NASA's pilot project with the City of Houston is summarized separately (visit https://toolkit.climate.gov/case-studies/climate-resilience to learn more).

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

West Virginia University Industrial Assessment Center (Final Progress Report)

The Industrial Assessment Center at West Virginia University has been successful in workforce development, and in generation of energy savings for manufacturing facilities during the period 2016 to 2021. Graduate and undergraduate students have benefited from energy assessment experience and most of them have found good positions as energy engineers and analysts in the industrial sector. Several peer reviewed research papers in archival journals as well as conference papers on the topic of energy engineering and assessment have been published. The implemented energy savings for manufacturing facilities have been significant in the areas of lighting, compressed air, process heating, steam, HVAC, chillers and cooling towers, and motors. In addition, water use reduction, smart manufacturing applications to save energy, cyber security evaluation, energy management, productivity improvements and waste reduction opportunities that lead to energy intensity reductions have been explored. The students have obtained an opportunity to interact with energy efficiency and productivity improvement professionals at various conferences and workshops and their research has generated important results. In summary, the West Virginia University Industrial Assessment Center (WVU-IAC) has fulfilled its mission in regard to workforce development, energy efficiency for manufacturing facilities, and laid a strong platform enhancing sustainability through reductions in carbon emissions achieved through energy efficiency and energy management initiatives and reductions in water usage and waste reduction. During the project period (2016-2021) the WVU-IAC has made numerous energy efficiency, water use reduction, waste reduction, and productivity improvement recommendations, a significant number of them having been implemented by the manufacturing facilities. The research adds significant understanding to the area of energy efficiency, water and waste reduction, and productivity improvement. The technical effectiveness and economic feasibility of the methods and techniques investigated and demonstrated through this project have been exemplary, resulting in significant recommended and implemented resource savings and reductions in carbon emissions. The project has been of significant benefit to the public owing to replication of results within the industrial sector, thus reducing operating costs for businesses that result in increase of growth and employment, as well as community benefits in terms of reductions in carbon emissions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Building and experimenting with an agent-based model to study the population-level impact of CommunityRx, a clinic-based community resource referral intervention

CommunityRx (CRx), an information technology intervention, provides patients with a personalized list of healthful community resources (HealtheRx). In repeated clinical studies, nearly half of those who received clinical “doses” of the HealtheRx shared their information with others (“social doses”). Clinical trial design cannot fully capture the impact of information diffusion, which can act as a force multiplier for the intervention. Furthermore, experimentation is needed to understand how intervention delivery can optimize social spread under varying circumstances. To study information diffusion from CRx under varying conditions, we built an agent-based model (ABM). This study describes the model building process and illustrates how an ABM provides insight about information diffusion through in silico experimentation. To build the ABM, we constructed a synthetic population (“agents”) using publicly-available data sources. Using clinical trial data, we developed empirically-informed processes simulating agent activities, resource knowledge evolution and information sharing. Using RepastHPC and chiSIM software, we replicated the intervention in silico, simulated information diffusion processes, and generated emergent information diffusion networks. The CRx ABM was calibrated using empirical data to replicate the CRx intervention in silico. We used the ABM to quantify information spread via social versus clinical dosing then conducted information diffusion experiments, comparing the social dosing effect of the intervention when delivered by physicians, nurses or clinical clerks. The synthetic population (N = 802,191) exhibited diverse behavioral characteristics, including activity and knowledge evolution patterns. In silico delivery of the intervention was replicated with high fidelity. Large-scale information diffusion networks emerged among agents exchanging resource information. Varying the propensity for information exchange resulted in networks with different topological characteristics. Community resource information spread via social dosing was nearly 4 fold that from clinical dosing alone and did not vary by delivery mode. This study, using CRx as an example, demonstrates the process of building and experimenting with an ABM to study information diffusion from, and the population-level impact of, a clinical information-based intervention. While the focus of the CRx ABM is to recreate the CRx intervention in silico, the general process of model building, and computational experimentation presented is generalizable to other large-scale ABMs of information diffusion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Soil viral production count, respiration, and amplicon data

This study aimed to quantify rates of viral production in aridisol soil under conditions as close to natural field soil as possible given the perturbations necessary to manipulate viral abundances. Viruses were removed from soil, then added back to virus-depleted soil to control the initial viral abundances at either 100% (field_abund) or 10% (reduced_abund) of measured field viral abundance to generate treatments with field-relevant and reduced viral infection pressure, respectively. Replicates of batch incubation jars were harvested every 8 hours for 48 hours to enumerate bacteria and viruses by microscopy (n=5) and profile bacterial community composition by 16S rRNA amplicon sequencing (n=3).

Zimmerman, Amy [Pacific Northwest National Laborat↗
DOE OSTI2017

Developing a Climate-Induced Social Vulnerability Index for Urban Areas: A Case Study of East Tennessee

Census American Community Survey 2008-2012 data are used to construct a spatially explicit Climate-Induced Social Vulnerability Index (CSVI) for the East Tennessee area. This CSVI is a combination of a Social Vulnerability Index (SVI) and a Climate Index. A method is replicated and adapted to derive a custom SVI by Census tract for the counties participating in the East Tennessee Index, and a Climate Index is developed for the same area based on indicators for climate hazards. The resulting datasets are exported as a raster to be integrated and combined within the Urban Climate Adaptation Tool (Urban-CAT) to act as an indicator for communities which may be differentially vulnerable to changes in climate. Results for the SVI are mapped separately from the complete CSVI in this document as results for the latter are in development.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards

Selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), is a data acquisition technique used in targeted analysis of molecules, including targeted proteomic studies. It exploits the unique capability of triple-quadrupole (QQQ) mass spectrometers to monitor the predefined precursor and fragment ion pairs of specific molecules of interest throughout a liquid chromatography (LC) elution profile. Compared to shotgun proteomics, targeted proteomics using SRM has high selectivity, high sensitivity, and a wide linear dynamic range,(1-3) which makes it especially useful in the accurate and reproducible quantification of low-abundance proteins in highly complex biological samples. SRM has been widely used in the fields of biomarker discovery,(4-7) analysis of protein post-translational modifications(8) and characterization of biological protein networks.(4,9) In the recent years, multiple technical advances have greatly improved the throughput of SRM analyses, allowing for the quantification of hundreds of peptides in a single analysis.(6,7,10) For example, a single 800-plex SRM assay (e.g., 400 unlabeled and heavy-labeled peptide pairs and 2400 transitions with retention time scheduling) using ultrahigh-performance liquid chromatography (UHPLC) has been developed to quantify proteins in plasma.(11) Advanced labeling techniques utilizing in vitro proteome-assisted MRM for protein absolute quantification (iMPAQT) demonstrated the capability of SRM in genome-wide protein quantification of over 18?000 human proteins.(12) Moreover, the scan speed of QQQ instrumentation has been greatly improved in recent releases of commercial instrumentation. The newly developed TSQ Altis (released in 2017) can scan more than 600 transitions per second, which is 6 times more than a traditional QQQ scan speed of 100 transitions per second. The breadth of measurement enabled by these technological improvements to QQQ mass spectrometry has increased the feasibility and popularity of large scale targeted proteomics studies,(13) a major application of which will be in clinical studies in which up to hundreds of protein candidates need to be quantified in hundreds of clinical specimens.(14) Quantitative accuracy is a primary motivating factor for utilizing a targeted proteomics protocol. The precise and reproducible absolute quantification produced by SRM assays is essential to many clinical and laboratory experiments.(15,16) Because the abundance of an endogenous peptide is calculated from the measurement of the spiked-in reference standard, it is essential to assess the data quality of these references.(17) In early applications of targeted proteomics, when instrument speed greatly limited the number of transitions that could be monitored, much of this quality assessment was done manually. However, recent improvements in instrument performance and experimental design have enabled a dramatic increase in the number of target peptides and associated SRM transitions, which makes manual quality assessment an untenable and laborious task. A variety of computational tools assist in SRM experiment design and data analysis. The first task in creating an SRM experiment is the choice of proteins and representative peptides to monitor. Achieving a reliable protein abundance requires appropriately choosing peptides that have a strong signal and are free from interferences in the biological matrix. Numerous computational tools exist to facilitate assay design by identifying peptides and refining SRM transitions.(18-21) To help share these assays and eliminate time spent designing the same transitions at multiple institutions, community portals have begun to host well-designed and vetted assays.(22-24) Analyzing the experimental data requires significant computational effort to align files across replicates and experimental conditions, pick peaks and produce quantitative values, normalize data and perform statistical tests, etc.(25-27)

Gibbons, Bryson C.↗
DOE OSTI2023

Long-term, large-scale experiment reveals the effects of seed limitation, climate, and anthropogenic disturbance on restoration of plant communities in a biodiversity hotspot

Ecological restoration is essential for maintaining biodiversity in the face of dynamic, global changes in climate, human land use, and disturbance regimes. Effective restoration requires understanding bottlenecks in plant community recovery that exist today, while recognizing that these bottlenecks may relate to complex histories of environmental change. Such understanding has been a challenge because few long-term, well-replicated experiments exist to decipher the demographic processes influencing recovery for numerous species against the backdrop of multiyear variation in climate and management. Here we address this challenge through a long-term and geographically expansive experiment in longleaf pine savannas, an imperiled ecosystem and biodiversity hotspot in the southeastern United States. Using 48 sites at three locations spanning 480 km, the 8-y experiment manipulated initial seed arrival for 24 herbaceous plant species and presence of competitors to evaluate the impacts of climate variability and management actions (e.g., prescribed burning) on plant establishment and persistence. Adding seeds increased plant establishment of many species. Cool and wet climatic conditions, low tree density, and reduced litter depth also promoted establishment. Once established, most species persisted for the duration of the 8-y experiment. Plant traits were most predictive when tightly coupled to the process of establishment. Our results illustrate how seed additions can restore plant diversity and how interannual climatic variation affects the dynamics of plant communities across a large region. The significant effects of temperature and precipitation inform how future climate may affect restoration and conservation via large-scale changes in the fundamental processes of establishment and persistence.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Montana Community-Scale Solar Strategy Project (Final Technical Report)

Grid-tied solar photovoltaic (PV) development began gradually in Montana, initially taking root in the early 2000s, largely in the form of small residential systems, rarely larger than two kilowatts. Utility support for solar technology through public benefit funding triggered the installation of the state’s first solar PV installations on community-owned facilities including schools, libraries, fire stations and local government buildings in the mid-2000s. By 2016, solar PV installations totaled approximately 28 megawatts of installed capacity, generating less than 0.05% of electricity sold in Montana. Montana’s solar fleet in 2016 included 17 megawatts of utility-scale solar farms, and three shared solar projects developed by rural electric cooperatives that ranged from 25 to 50 kilowatts in size. However, with only 3,000 households utilizing solar PV, either through an on-site installation or participation in a shared solar project, the potential benefits and reach of solar technology was limited. The Montana Solar Community Project (MSCP) was developed by the Montana Energy Office (MEO) at the Department of Environmental Quality in order to implement a “community-scale” solar energy strategy for the state that would cost-effectively expand Montanans’ access to solar PV. This project defines three types of community-scale solar projects: shared solar, community-sited solar, and group purchasing programs. The MSCP project conducted research and stakeholder engagement that helped to inform and develop model community-scale initiatives and an overarching community-scale solar strategy for Montana. Specifically, the project included a solar market assessment, stakeholder meetings across Montana, development of a menu of community-scale solar options, a study of solar potential on schools, community solar market research, and community-scale project implementation support. MSCP activities were successful in implementing solar projects and supporting solar development in communities across Montana. Project activities realized 280 kW of newly installed solar from two solarize programs, a shared solar array at a rural electric cooperative, and a solar array atop a Bozeman high school. The community-scale project implementation support and Solar on Schools components of the project resulted directly in the analysis and design of nearly 2 MW of distributed solar systems across the state. The Solar on Schools analysis alone produced solar designs for 25 schools, representing 920.8 kW of solar potential. Many of the deliverables from this project provide guidance on future development of community-scale solar in Montana, and resulted in a number of important conclusions about community-scale solar in Montana. There is strong interest in community-scale solar in Montana, as noted during stakeholder meetings, in response to solar market research surveys, and as seen by applications for implementation support grants provided by MEO. Project activities also suggest that Montanans demonstrated a desire and need for more information about solar energy technology, solar financing options, and the state’s policy and regulatory framework. Additionally, the project found that schools will be key partners for future community-scale solar programs. In addition to being excellent hosts for solar arrays, schools have the opportunity to use the installation of a solar array to develop educational materials and curricula to educate Montana’s future leaders about these technologies, which can be shared and replicated across the state. Project activities laid a clear path forward for solar energy in Montana. Certain activities have concrete next steps. For example, numerous solar arrays were designed for schools and other public buildings around the state. Many of those designs will be used as soon as funding becomes available. Other activities have less developed next steps, though lay the foundation for future work. The solar market assessment, solar market research, and community stakeholder meetings are good examples. These documents can be used as stepping stones to increase renewable energy education, increase stakeholder outreach, and support communities as they seek to develop community-scale solar projects.

14 SOLAR ENERGY↗
DOE OSTI2018

Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H 2 18 O

Growing bacteria have a high concentration of ribosomes to ensure sufficient protein synthesis, which is necessary for genome replication and cellular division. To elucidate whether metabolic activity of soil microorganisms is coupled with growth, we investigated the relationship between rRNA and DNA synthesis in a soil bacterial community using quantitative stable isotope probing (qSIP) with H 2 18 O. Most soil bacterial taxa were metabolically active and grew, and there was no significant difference between the isotopic composition of DNA and RNA extracted from soil incubated with H 2 18 O. The positive correlation between 18 O content of DNA and rRNA of taxa, with a slope statistically indistinguishable from 1 (slope = 0.96; 95% confidence interval [CI], 0.90 to 1.02), indicated that few taxa made new rRNA without synthesizing new DNA. There was no correlation between rRNA-to-DNA ratios obtained from sequencing libraries and the atom percent excess (APE) 18 O values of DNA or rRNA, suggesting that the ratio of rRNA to DNA is a poor indicator of microbial growth or rRNA synthesis. Our results support the notion that metabolic activity is strongly coupled to cellular division and suggest that nondividing taxa do not dominate soil metabolic activity. IMPORTANCE: Utilizing quantitative stable isotope probing of microbial RNA and DNA with H 2 18 O, we show that most soil taxa are metabolically active and grow because their nucleic acids are significantly labeled with 18 O. A majority of the populations that make new rRNA also grow, which argues against the common paradigm that most soil taxa are dormant. Moreover, our results indicate that relative sequence abundance-based RNA-to-DNA ratios, which are frequently used for identifying active microbial populations in the environment, underestimate the number of metabolically active taxa within soil microbial communities.

environmental microbiology↗
DOE OSTI2016

SPRUCE Deep Peat Heating (DPH) Peat Water Content and Temperature for Experimental Plot Cores, June 2014 through June 2015

This data set provides the peat water content and peat temperature at time of sampling for peat cores collected before and during the SPRUCE Deep Peat Heating (DPH) study. Cores were collected during three sampling events: 03 June 2014, 09 September 2014, and 16 June 2015. Two cores were extracted from hollow locations in each of the 10 experimental plots (4, 6, 8, 10, 11, 13, 16, 17, 19, and 20). The five ambient plots (5, 7, 14, and 21) were not included in the DPH sampling efforts. See Table 1. Cores were partitioned into samples at 11 depth increments: 0-10, 10-20, 20-30, 30-40, 40-50, 50-75, 75-100, 100-125, 125-150, 150-175, and 175-200 cm below surface of the hollow. The DPH study was undertaken to evaluate possible rapid responses of deep peat carbon (C) stocks, microbial communities, and biogeochemical cycling processes to unprecedented temperatures. In June 2014, deep soil heating was initiated at 5 warming levels (+0, +2.25, +4.5, +6.75 and +9 °C) with 2 replicate plots per level. Warming levels at depth were achieved over a 25 (+ 2.25 °C) to 60-day (+9 °C) period depending on the target treatment temperatures. Data file – There is one comma-separated (*.csv) file with peat core water content and temperature at time of sampling, plus the amount of dried archived material retained after analyses. User Note: In this third release, four variables related to extrapolations of peat core temperature were removed. See the Data Set History table for additional details. 25-150, 150-175, and 175-200 cm below surface of the hollow.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Reproducibility, Replicability, and Research Quality in Homogeneous Catalysis

Researchers from all sectors of homogeneous catalysis convened in response to concerns regarding reproducibility in science to analyze the issue and provide recommendations. In addition to an in- person workshop, the group engaged the broader homogeneous catalysis community through a webinar series and virtually during the workshop. Results of the project affirm that homogeneous catalysis is not in a reproducibility crisis, as evidenced by the field’s current and past contributions to society that have led to economic growth and advances in a range of industries from agriculture to consumer goods to human health. However, it is not uncommon for researchers to encounter obstacles related to reproducibility. Ensuring reproducibility remains the responsibility of the community, both in current work and in training future researchers. This report is intended to engage key stakeholders, including disciplinary societies, publishers, employers, research leaders, and researchers, in practices that maximize reproducible homogeneous catalysis and ensure continued innovation and translatable discoveries. Recommendations made herein are also framed to be applicable beyond homogeneous catalysis, empowering the broader chemical if not scientific community.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Community composition and abundance of wild bees at row crop-grassland interfaces in west central Nebraska

Abstract Perennial mixed forb and grassland habitats are crucial to conservation of pollinators and connectivity of habitats in intensely farmed landscapes. This study aims to understand the effects of land use on the pollinator community by describing bee abundance, species richness and community composition in perennial conservation grasslands and adjacent annual row crops located in west central Nebraska. In 2022 and 2023, we collected and identified bees via sticky traps at 4 locations (center and edge of adjacent grasslands and crop fields) at 6 replicated sites. We collected 1,768 specimens from sticky traps, resulting in 70 species within 28 genera. Halictidae accounted for 84% of the specimens collected. Bee abundance was influenced by the simple effects of land use (grassland vs. crops), edge adjacency, and the month and year of collection. Differences in bee abundance within a collection date were found mostly in early 2022 (May and June) and late 2023 (September), when the crop center location was generally the lowest, with some evidence for spillover of bees from the grassland into the crop edge during the early summer months. Bee species richness was affected only by month and was not significantly different by land use and edge adjacency. Bee community composition overlapped across the 4 locations, although there were significant dissimilarities between crop fields and grasslands. Surveys of the plant community revealed very low abundance of blooming stems and plant taxonomic richness at crop locations for all sampling periods, while grassland locations were comparatively high and varied over time. Plant communities showed no overlap between crop field and grassland locations. Overall, we found that conservation grasslands, while not seeded specifically with pollinator-attractive forbs, provide diverse resources to support wild bee communities in west central Nebraska; crop edges may also provide non-plant resources such as nesting sites and irrigation water. Going forward, better understanding pollinator species composition and resource utilization relative to land use characteristics and drought conditions will allow for better tailoring of conservation efforts and management strategies in Nebraska and across the larger region.

Entomology↗
DOE OSTI2021

Revisiting the unique structure of autonomously replicating sequences in Yarrowia lipolytica and its role in pathway engineering

Production of industrially relevant compounds in microbial cell factories can employ either genomes or plasmids as an expression platform. Selection of plasmids as pathway carriers is advantageous for rapid demonstration but poses a challenge of stability. Yarrowia lipolytica has attracted great attention in the past decade for the biosynthesis of chemicals related to fatty acids at titers attractive to industry, and many genetic tools have been developed to explore its oleaginous potential. Here, our recent studies on the autonomously replicating sequences (ARSs) of nonconventional yeasts revealed that the ARSs from Y. lipolytica showcase a unique structure that includes a previously unannotated sequence (spacer) linking the origin of replication (ORI) and the centromeric (CEN) element and plays a critical role in modulating plasmid behavior. Maintaining a native 645-bp spacer yielded a 2.2-fold increase in gene expression and 1.7-fold higher plasmid stability compared to a more universally employed minimized ARS. Testing the modularity of the ARS sub-elements indicated that plasmid stability exhibits a pronounced cargo dependency. Instability caused both plasmid loss and intramolecular rearrangements. Altogether, our work clarifies the appropriate application of various ARSs for the scientific community and sheds light on a previously unexplored DNA element as a potential target for engineering Y. lipolytica.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

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

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

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

DelPlasmid: Finding Plasmids with Deep Learning and Machine Learning v1

Extrachromosomal genetic elements or plasmids are an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from host cell chromosomes and their frequent self-transfer. In recent years, the Department of Energy has recognized the importance of plasmid DNA to the viability and success of microbial communities and JGI has responded with funding to support the research and development of new methods and tools for the efficient sequencing of plasmid DNA. LBNL #2019-037 is responsive to this call.

Andreopoulos, William↗