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DOE OSTI2024

Dynamic data-driven multiscale modeling for predicting the degradation of a 316L stainless steel nuclear cladding material

Here, we have developed a long short-term memory stacked ensemble (LSTM-SE) surrogate modeling approach that can provide rapid predictions of microstructural evolution and the resultant mechanical properties of American Iron and Steel Institute (AISI) 316L series stainless steel (316LSS) fuel cladding under conditions of varying temperature and radiation dose rate. To acquire training data, we developed and implemented a kinetic Monte Carlo (KMC) model to simulate precipitation kinetics of M 23 C 6 , γ', and G phases within SS316L cladding. Experimentally reported precipitation kinetics of SS316L in literature were linked to the kinetic parameters of the simulated precipitation in our KMC model. The model was then used to simulate microstructure evolution under synthetically generated treatments of varying temperature and radiation dose rate, for periods of up to 3000 hours. Changes in volume fraction, number density, and particle size of precipitates were recorded, and particle area fractions were correlated using statistical methods to develop the surrogate model. Simultaneously, the mechanical properties of the simulated microstructures were evaluated using microstructure-based finite element method (FEM) analysis to determine the elastic modulus, yield stress, ultimate tensile strength, and elongation to failure of the aged microstructures. Using this approach, our surrogate model can predict precipitation behavior within 0.25% volume fraction and mechanical properties within 6% relative error from the values predicted by the KMC and FEM models using 50 training simulations as input. The trained recurrent neural network-based model can return estimations of precipitation kinetics and mechanical properties ~1000 times faster than the physics-based codes. This work demonstrates, as a proof of concept, that reactor material service lifetimes under variable service conditions can be predicted for a statistics-based model from a practicably obtainable dataset.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum

Abstract Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Photosynthetic modulation during the diurnal cycle in a unicellular diazotrophic cyanobacterium grown under nitrogen-replete and nitrogen-fixing conditions

Abstract Cyanobacteria are the only oxygenic photosynthetic organisms that can fix nitrogen. In diazotrophic cyanobacteria, the regulation of photosynthesis during the diurnal cycle is hypothesized to be linked with nitrogen fixation and involve the D1 protein isoform PsbA4. The amount of bioavailable nitrogen has a major impact on productivity in aqueous environments. In contrast to low- or nitrogen-fixing (−N) conditions, little data on photosynthetic regulation under nitrogen-replete (+ N) conditions are available. We compared the regulation of photosynthesis under −N and + N conditions during the diurnal cycle in wild type and a psbA4 deletion strain of the unicellular diazotrophic cyanobacterium Cyanothece sp. ATCC 51142. We observed common changes to light harvesting and photosynthetic electron transport during the dark in + N and −N conditions and found that these modifications occur in both diazotrophic and non-diazotrophic cyanobacteria. Nitrogen availability increased PSII titer when cells transitioned from dark to light and promoted growth. Under −N conditions, deletion of PsbA4 modified charge recombination in dark and regulation of PSII titer during dark to light transition. We conclude that darkness impacts the acceptor-side modifications to PSII and photosynthetic electron transport in cyanobacteria independently of the nitrogen-fixing status and the presence of PsbA4.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Theoretical foundations of waste factor and waste figure with applications to fixed wireless access and relay systems

The growing energy demands of next-generation wireless systems call for unified, system-level metrics to evaluate and optimize energy efficiency. This paper advances the concept of the Waste Factor (W), or Waste Figure (WF) in decibel scale, as a general framework for modeling power loss across cascaded communication components. By integrating W into the Consumption Factor (CF)–the ratio of data rate to consumed power–we reveal how component inefficiencies influence the minimum achievable energy per bit. Closed-form expressions are derived for energy-per-bit consumption in both direct and relay-assisted links, along with a decision rule for selecting the more energy-efficient path. While not explicitly modeled, Reflective Intelligent Surfaces (RIS) are shown to fit naturally within this framework. The analysis is further applied to a Fixed Wireless Access (FWA) scenario, where asymmetries in traffic direction and hardware inefficiencies are jointly considered, demonstrating the utility of the Waste Factor in guiding energy-aware system design.

Sevim, Nurullah [Texas A&M University, College Sta↗

DOE OSTI2020

Review: knots and other new topological effects in liquid crystals and colloids

Abstract Humankind has been obsessed with knots in religion, culture and daily life for millennia, while physicists like Gauss, Kelvin and Maxwell already involved them in models centuries ago. Nowadays, colloidal particles can be fabricated to have shapes of knots and links with arbitrary complexity. In liquid crystals, closed loops of singular vortex lines can be knotted by using colloidal particles and laser tweezers, as well as by confining nematic fluids into micrometer-sized droplets with complex topology. Knotted and linked colloidal particles induce knots and links of singular defects, which can be interlinked (or not) with colloidal particle knots, revealing the diversity of interactions between topologies of knotted fields and topologically nontrivial surfaces of colloidal objects. Even more diverse knotted structures emerge in nonsingular molecular alignment and magnetization fields in liquid crystals and colloidal ferromagnets. The topological solitons include hopfions, skyrmions, heliknotons, torons and other spatially localized continuous structures, which are classified based on homotopy theory, characterized by integer-valued topological invariants and often contain knotted or linked preimages, nonsingular regions of space corresponding to single points of the order parameter space. A zoo of topological solitons in liquid crystals, colloids and ferromagnets promises new breeds of information displays and a plethora of data storage, electro-optic and photonic applications. Their particle-like collective dynamics echoes coherent motions in active matter, ranging from crowds of people to schools of fish. This review discusses the state of the art in the field, as well as highlights recent developments and open questions in physics of knotted soft matter. We systematically overview knotted field configurations, the allowed transformations between them, their physical stability and how one can use one form of knotted fields to model, create and imprint other forms. The large variety of symmetries accessible to liquid crystals and colloids offer insights into stability, transformation and emergent dynamics of fully nonsingular and singular knotted fields of fundamental and applied importance. The common thread of this review is the ability to experimentally visualize these knots in real space. The review concludes with a discussion of how the studies of knots in liquid crystals and colloids can offer insights into topologically related structures in other branches of physics, with answers to many open questions, as well as how these experimentally observable knots hold a strong potential for providing new inspirations to the mathematical knot theory.

Physics↗

DOE OSTI2025

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations

Abstract Motivation Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in noncoding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data. Results We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of nonrandom interactions from all Hi-C interactions. Using these nonrandom interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization. Availability and implementation It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci.

Du, Lin (ORCID:0009000289869812)↗

DOE OSTI2020

SDSS-IV MaNGA: The kinematic-morphology of galaxies on the mass versus star-formation relation in different environments

ABSTRACT We study the link between the kinematic-morphology of galaxies, as inferred from integral-field stellar kinematics, and their relation between mass and star formation rate. Our sample consists of ∼3200 galaxies with integral-field spectroscopic data from the MaNGA survey (Mapping Nearby Galaxies at Apache Point Observatory) with available determinations of their effective stellar angular momentum within the half-light radius $\lambda _{R_e}$. We find that for star-forming galaxies, namely along the star formation main sequence (SFMS), the $\lambda _{R_e}$ values remain large and almost unchanged over about two orders of magnitude in stellar mass, with the exception of the lowest masses $\mathcal {M}_{\star }\lesssim 2\times 10^{9} \, \mathcal {M}_{\odot }$, where $\lambda _{R_e}$ slightly decreases. The SFMS is dominated by spiral galaxies with small bulges. Below the SFMS, but above the characteristic stellar mass $\mathcal {M}_{\rm crit}\approx 2\times 10^{11} \, \mathcal {M}_{\odot }$, there is a sharp decrease in $\lambda _{R_e}$ with decreasing star formation rate (SFR): massive galaxies well below the SFMS are mainly slow-rotator early-type galaxies, namely genuinely spheroidal galaxies without discs. Below the SFMS and below $\mathcal {M}_{\rm crit}$ the decrease of $\lambda _{R_e}$ with decreasing SFR becomes modest or nearly absent: low-mass galaxies well below the SFMS, are fast-rotator early-type galaxies, and contain fast-rotating stellar discs like their star-forming counterparts. We also find a small but clear environmental dependence for the massive galaxies: in the mass range $10^{10.9}\!-\!10^{11.5} \, \mathcal {M}_{\odot }$, galaxies in rich groups or denser regions or classified as central galaxies have lower values of $\lambda _{R_e}$. While no environmental dependence is found for galaxies of lower mass. We discuss how the above results can be understood as due to the different star formation and mass assembly histories of galaxies with varying mass.

Wang, Bitao↗

DOE OSTI2021

Anonymization of Network Traces Data through Condensation-based Differential Privacy

Network traces are considered a primary source of information to researchers, who use them to investigate research problems such as identifying user behavior, analyzing network hierarchy, maintaining network security, classifying packet flows, and much more. However, most organizations are reluctant to share their data with a third party or the public due to privacy concerns. Therefore, data anonymization prior to sharing becomes a convenient solution to both organizations and researchers. Although several anonymization algorithms are available, few of them allow sufficient privacy (organization need), acceptable data utility (researcher need), and efficient data analysis at the same time. This article introduces a condensation-based differential privacy anonymization approach that achieves an improved tradeoff between privacy and utility compared to existing techniques and produces anonymized network trace data that can be shared publicly without lowering its utility value. Our solution also does not incur extra computation overhead for the data analyzer. A prototype system has been implemented, and experiments have shown that the proposed approach preserves privacy and allows data analysis without revealing the original data even when injection attacks are launched against it. When anonymized datasets are given as input to graph-based intrusion detection techniques, they yield almost identical intrusion detection rates as the original datasets with only a negligible impact.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

INGENIOUS - Great Basin Regional Dataset Compilation

This is the regional dataset compilation for the INnovative Geothermal Exploration through Novel Investigations Of Undiscovered Systems (INGENIOUS) project. The primary goal of this project is to accelerate discoveries of new, commercially viable hidden geothermal systems while reducing the exploration and development risks for all geothermal resources. These datasets will be used in INGENIOUS as input features for predicting geothermal favorability throughout the Great Basin study area. Datasets consist of shapefiles, geotiffs, tabular spreadsheets, and metadata that describe: 2-meter temperature probe surveys, quaternary faults and volcanic features, geodetic shear and dilation models, heat flow, magnetotellurics (conductance), magnetics, gravity, paleogeothermal features (such as sinter and tufa deposits), seismicity, spring and well temperatures, spring and well aqueous geochemistry analyses, thermal conductivity, and fault slip and dilation tendency. For additional project information, see the INGENIOUS project site linked in the submission. Terms of use: These datasets are provided "as is", and the contributors assume no responsibility for any errors or omissions. The user assumes the entire risk associated with their use of these data and bears all responsibility in determining whether these data are fit for their intended use. These datasets may be redistributed with attribution (see citation information below). Please refer to the license information on this page for full licensing terms and conditions.

15 GEOTHERMAL ENERGY↗

DOE OSTI2022

Dynamic Data-Driven Multiscale Modeling for Predicting Microstructure and Mechanical Properties of 316L Stainless Steel

We have developed a long short-term memory stacked ensemble (LSTM-SE) surrogate modeling approach that can provide rapid predictions of microstructural evolution and the resultant mechanical properties of American Iron and Steel Institute (AISI) 316L series stainless steel (316LSS) fuel cladding under conditions of varying temperature and radiation dose rate. To acquire training data, we developed and implemented a kinetic Monte Carlo (KMC) model to simulate precipitation kinetics of M 23 C 6 , γ', and G phases within SS316L cladding. Experimentally reported precipitation kinetics of SS316L in literature were linked to the kinetic parameters of the simulated precipitation in our KMC model. The model was then used to simulate microstructure evolution under synthetically generated treatments of varying temperature and radiation dose rate, for periods of up to 3000 hours. Changes in volume fraction, number density, and particle size of precipitates were recorded, and particle area fractions were correlated using statistical methods to develop the surrogate model. Simultaneously, the mechanical properties of the simulated microstructures were evaluated using microstructure-based finite element method (FEM) analysis to determine the elastic modulus, yield stress, ultimate tensile strength, and elongation to failure of the aged microstructures. Using this approach, our surrogate model can predict precipitation behavior within 0.25% volume fraction and mechanical properties within 6% relative error from the values predicted by the KMC and FEM models using 50 training simulations as input. The trained recurrent neural network-based model can return estimations of precipitation kinetics and mechanical properties ~1000 times faster than the physics-based codes. This work demonstrates, as a proof of concept, that reactor material service lifetimes under variable service conditions can be predicted for a statistics-based model from a practicably obtainable dataset.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Global disease burden linked to diet high in red meat and colorectal cancer from 1990 to 2019 and its prediction up to 2030

Background Numerous studies have already identified an association between excessive consumption of red meat and colorectal cancer (CRC). However, there has been a lack of detailed understanding regarding the disease burden linked to diet high in red meat and CRC. Objective We aim to offer evidence-based guidance for developing effective strategies that can mitigate the elevated CRC burden in certain countries. Methods We used the data from the Global Burden of Disease (GBD) Study 2019 to evaluate global, regional, and national mortality rates and disability-adjusted Life years (DALYs) related to diet high in red meat. We also considered factors such as sex, age, the socio-demographic index (SDI), and evaluated the cross-national inequalities. Furthermore, we utilized DALYs data from 204 countries and regions to measure cross-country inequalities of CRC by calculating the slope index of inequality and concentration index as standard indicators of absolute and relative inequalities. Discussion The results show that globally, the age-standardized mortality rate (ASMR) and age-standardized disability adjusted life year rate (ASDR) related to CRC due to diet high in red meat have decreased, with estimated annual percent change (EAPCs) of −0.32% (95% CI −0.37 to −0.28) and-0.18% (95% CI −0.25 to −0.11). Notably, the burden was higher among males and the elderly. The slope index of inequality rose from 22.0 (95% CI 18.1 to 25.9) in 1990 to 32.9 (95% CI 28.3 to 37.5) in 2019 and the concentration index fell from 59.5 (95% CI 46.4 to 72.6) in 1990 to 48.9 (95% CI 34.6 to 63.1) in 2019. Also, according to our projections, global ASDR and ASMR might tend to increase up to 2030. Conclusion ASMR and ASDR for CRC associated with high red meat diets declined globally from 1990 to 2019, but the absolute number of cases is still rising, with men and the elderly being more affected. CRC associated with diets high in red meat exhibits significant income inequality, placing a disproportionate burden on wealthier countries. Moreover, according to our projections, ASMR and ASDR are likely to increase globally by 2030. In order to address this intractable disease problem, understanding changes in global and regional epidemiologic trends is critical for policy makers and others.

Yang, Xuesong↗

DOE OSTI2023

Assessing carbon storage capacity and saturation across six central US grasslands using data–model integration

Abstract. Future global changes will impact carbon (C) fluxes and pools in most terrestrial ecosystems and the feedback of terrestrial carbon cycling to atmospheric CO2. Determining the vulnerability of C in ecosystems to future environmental change is thus vital for targeted land management and policy. The C capacity of an ecosystem is a function of its C inputs (e.g., net primary productivity – NPP) and how long C remains in the system before being respired back to the atmosphere. The proportion of C capacity currently stored by an ecosystem (i.e., its C saturation) provides information about the potential for long-term C pools to be altered by environmental and land management regimes. We estimated C capacity, C saturation, NPP, and ecosystem C residence time in six US grasslands spanning temperature and precipitation gradients by integrating high temporal resolution C pool and flux data with a process-based C model. As expected, NPP across grasslands was strongly correlated with mean annual precipitation (MAP), yet C residence time was not related to MAP or mean annual temperature (MAT). We link soil temperature, soil moisture, and inherent C turnover rates (potentially due to microbial function and tissue quality) as determinants of carbon residence time. Overall, we found that intermediates between extremes in moisture and temperature had low C saturation, indicating that C in these grasslands may trend upwards and be buffered against global change impacts. Hot and dry grasslands had greatest C saturation due to both small C inputs through NPP and high C turnover rates during soil moisture conditions favorable for microbial activity. Additionally, leaching of soil C during monsoon events may lead to C loss. C saturation was also high in tallgrass prairie due to frequent fire that reduced inputs of aboveground plant material. Accordingly, we suggest that both hot, dry ecosystems and those frequently disturbed should be subject to careful land management and policy decisions to prevent losses of C stored in these systems.

58 GEOSCIENCES↗

DOE OSTI2023

Deterministic-Monte Carlo Hybrid Methods for Eigenvalue Sensitivity Coefficient Calculations

The TSUNAMI suite within the SCALE code package includes several methods for generating sensitivity data, including multigroup (MG) and continuous-energy (CE) capabilities. For generating sensitivities with CE data, three methods are available in SCALE 6.3.0: (1) the iterated fission probability (IFP) method with the KENO Monte Carlo transport solver, (2) IFP with the Shift Monte Carlo transport solver, and (3) the Contributon-Linked eigenvalue sensitivity/Uncertainty estimation via Tracklength importance Characterization (CLUTCH) with the KENO Monte Carlo transport solver. Currently, it is difficult to generate accurate sensitivities with large reflectors when using the CLUTCH method, specifically with fissionable and hydrogenous materials. To address this issue, the work presented herein examines a methodology to calculate the adjoint flux externally with the 3D deterministic SN transport code DENOVO in SCALE; the result is then read directly into the CLUTCH-TSUNAMI sequence. This hybridization method replaces the Monte Carlo F*(r) calculation in CLUTCH while still utilizing the forward calculation. The critical benchmark HEU-MET-FAST-028-001 is used to generate sensitivities based on the inability of CLUTCH to generate accurate sensitivities. Results from the hybrid method appear to generate sensitivity values that are in excellent agreement with direct perturbations. Although further testing is needed, the method provides promising results for the development and utility of a hybrid method for use in TSUNAMI.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Examining Rail Transportation Route of Crude Oil in the United States Using Crowdsourced Social Media Data

Safety issues associated with transporting crude oil by rail have been a concern since the boom of the U.S. domestic shale oil production in 2012. During the last decade, over 300 crude-oil-by-rail incidents have occurred in the United States. Some of them have caused adverse consequences including fire and hazardous materials leakage. However, only limited information on crude-on-rail routes and their associated risks is available to the public. To this end, this study proposed an unconventional way to reconstruct crude-on-rail routes using geotagged photos harvested from the Flickr website. The proposed method linked the geotagged photos of crude oil trains posted online with national railway networks to identify potential railway segments that those crude oil trains were traveling on. Here, a shortest path-based method was applied to infer the complete crude-on-rail routes, by utilizing the confirmed railway segments as well as their directional information. Validation of the inferred routes was performed using a public map and official crude oil incident data. The results suggested that the inferred routes based on geotagged photos had high coverage, with approximately 96% of the documented crude oil incidents aligned with the reconstructed crude-on-rail network. The inferred crude oil train routes were found to pass through several metropolitan areas of high population density, who were exposed to potential risk. These findings could improve situational awareness for policy makers and transportation planners. In addition, with the inferred routes, this study has established a good foundation for future crude oil train risk-analyses along the rail route.

42 ENGINEERING↗

DOE OSTI2024

Offshore Wind Composite Siting Exclusions Scenarios

This dataset consolidates criteria that restrict the siting of offshore wind energy installations, an update from Zuckerman et al. (2023). All scenarios exclude area from wind energy development due to legal or administrative restrictions (e.g., Marine Protected Areas), existing infrastructure, and technical constraints (e.g., 1,300 m bathymetry limit). A TIF data file and a PNG cartographic map of the data are provided for three scenarios ("Open", "Reference", and "Limited"), showing areas where offshore wind energy is restricted across the contiguous United States. The "Open" scenario only excludes areas with known preclusions for offshore wind deployment. The "Reference" scenario excludes all areas from the "Open" scenario, as well as additional best management practices such as known proposed protected areas, and state waters. The "Limited" scenario excludes all area from the "Reference" scenario. Additionally, it has more stringent siting criteria such as larger setbacks from shore and infrastructure, as well as shallower depth limits on floating technology. For further details and citation, please refer to the publication linked below: Zuckerman, Gabriel R., Anthony Lopez, Travis Williams, Rebecca Green, and Grant Buster. 2023. Impacts of Siting Considerations on Offshore Wind Technical Potential in the United States. Golden, CO: National Renewable Energy Laboratory. NREL/TP-6A20- 85088.

Array↗

DOE OSTI2025

A mesoscopic link-transmission-model able to track individual vehicles

Macroscopic traffic flow is a common choice for large-scale traffic simulations. These models do not provide individual-specific metrics as outputs. However, this treatment is necessary in agent-based-models, as in, for example, assigning routes based on personal characteristics. Here, in this paper, we propose an extension of the link-transmission-model, an efficient and yet accurate discretization of the Lighthill-Whitham-Richards (LWR) model, which allow vehicles to be tracked individually while keeping the main features of the underlying model. The extension comprises modifying the link and node models to ensure that the flow between links is always at discrete levels. Therefore, every unit of flow is associated with one individual vehicle moving from its current to its next link. An upper bound of the discretization error is provided. We show that the proposed model resembles its continuous counterpart on lane drop, merge, and diverge cases. In addition, we apply the model into three different networks to validate its applicability in large networks. Finally, we also confirm the parameter transferability between continuous and discrete models and that both can well reproduce field data.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. In this work, we demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Examining the Relationship Between the Testate Amoeba Hyalosphenia papilio (Arcellinida, Amoebozoa) and its Associated Intracellular Microalgae Using Molecular and Microscopic Methods

Symbiotic relationships between heterotrophic and phototrophic partners are common in microbial eukaryotes. Among Arcellinida (Amoebozoa) several species are associated with microalgae of the genus Chlorella (Archaeplastida). So far, these symbioses were assumed to be stable and mutualistic, yet details of the interactions are limited. Here, we analyzed 22 single-cell transcriptomes and 36 partially-sequenced genomes of the Arcellinida morphospecies Hyalosphenia papilio, which contains Chlorella algae, to shed light on the amoeba-algae association. By characterizing the genetic diversity of associated Chlorella, we detected two distinct clades that can be linked to host genetic diversity, yet at the same time show a biogeographic signal across sampling sites. Fluorescence and transmission electron microscopy showed the presence of intact algae cells within the amoeba cell. Yet analysis of transcriptome data suggested that the algal nuclei are inactive, implying that instead of a stable, mutualistic relationship, the algae may be temporarily exploited for photosynthetic activity before being digested. Furthermore, differences in gene expression of H. papilio and Hyalosphenia elegans demonstrated increased expression of genes related to oxidative stress. Together, our analyses increase knowledge of this host-symbiont association and reveal 1) higher diversity of associated algae than previously characterized, 2) a transient association between H. papilio and Chlorella with unclear benefits for the algae, 3) algal-induced gene expression changes in the host.

59 BASIC BIOLOGICAL SCIENCES↗