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At least 55 records · Page 3

Conservation of Species- and Trait-Based Modeling Network Interactions in Extremely Acidic Microbial Community Assembly

Understanding microbial interactions is essential to decipher the mechanisms of community assembly and their effects on ecosystem functioning, however, the conservation of species- and trait-based network interactions along environmental gradient remains largely unknown. Here, by using the network-based analyses with three paralleled data sets derived from 16S rRNA gene pyrosequencing, functional microarray, and predicted metagenome, we test our hypothesis that the network interactions of traits are more conserved than those of taxonomic measures, with significantly lower variation of network characteristics along the environmental gradient in acid mine drainage. The results showed that although the overall network characteristics remained similar, the structural variation was significantly lower at trait levels. The higher conserved individual node topological properties at trait level rather than at species level indicated that the responses of diverse traits remained relatively consistent even though different species played key roles under different environmental conditions. Additionally, the randomization tests revealed that it could not reject the null hypothesis that species-based correlations were random, while the tests suggested that correlation patterns of traits were non-random. Furthermore, relationships between trait-based network characteristics and environmental properties implied that trait-based networks might be more useful in reflecting the variation of ecosystem function. Taken together, our results suggest that deterministic trait-based community assembly results in greater conservation of network interaction, which may ensure ecosystem function across environmental regimes, emphasizing the potential importance of measuring the complexity and conservation of network interaction in evaluating the ecosystem stability and functioning.

59 BASIC BIOLOGICAL SCIENCES↗

Insights into the variability of nucleated amyloid polymerization by a minimalistic model of stochastic protein assembly

Self-assembly of proteins into amyloid aggregates is an important biological phenomenon associated with human diseases such as Alzheimer’s disease. Amyloid fibrils also have potential applications in nano-engineering of biomaterials. The kinetics of amyloid assembly show an exponential growth phase preceded by a lag phase, variable in duration as seen in bulk experiments and experiments that mimic the small volumes of cells. Here, to investigate the origins and the properties of the observed variability in the lag phase of amyloid assembly currently not accounted for by deterministic nucleation dependent mechanisms, we formulate a new stochastic minimal model that is capable of describing the characteristics of amyloid growth curves despite its simplicity. We then solve the stochastic differential equations of our model and give mathematical proof of a central limit theorem for the sample growth trajectories of the nucleated aggregation process. These results give an asymptotic description for our simple model, from which closed form analytical results capable of describing and predicting the variability of nucleated amyloid assembly were derived. We also demonstrate the application of our results to inform experiments in a conceptually friendly and clear fashion. Our model offers a new perspective and paves the way for a new and efficient approach on extracting vital information regarding the key initial events of amyloid formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome

Microbial community assembly is affected by a combination of forces that act simultaneously, but the mechanisms underpinning their relative influences remain elusive. This gap strongly limits our ability to predict human impacts on microbial communities and the processes they regulate. Here, we experimentally demonstrate that increased salinity stress, food web alteration and nutrient loading interact to drive outcomes in salt marsh fungal leaf communities. Both salinity stress and food web alterations drove communities to deterministically diverge, resulting in distinct fungal communities. Increased nutrient loads, nevertheless, partially suppressed the influence of other factors as determinants of fungal assembly. Using a null model approach, we found that increased nutrient loads enhanced the relative importance of stochastic over deterministic divergent processes; without increased nutrient loads, samples from different treatments showed a relatively (deterministic) divergent community assembly whereas increased nutrient loads drove the system to more stochastic assemblies, suppressing the effect of other treatments. These results demonstrate that common anthropogenic modifications can interact to control fungal community assembly. As a result, our results suggest that when the environmental conditions are spatially heterogeneous (as in our case, caused by specific combinations of experimental treatments), increased stochasticity caused by greater nutrient inputs can reduce the importance of deterministic filters that otherwise caused divergence, thus driving to microbial community homogenization.

54 ENVIRONMENTAL SCIENCES↗

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

Increasing evidence emerged for non-random spatial distributions for microbes, but the underlying processes resulting in microbial assemblage variation among and within Earth’s ecosystems is still lacking. For instance, some studies showed that the deterministic processes by habitat specialization are important, while other studies hold that bacterial communities are assembled by neutral forces. Here we examine the relative importance of deterministic and stochastic processes for bacterial communities from subsurface environments, as well as stream biofilm, lake water, lake sediment and soil using pyrosequencing of 16S rRNA gene. We show that there is a general pattern in phylogenetic signal in species niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups, and for three sample groups, that spatial distance reflects unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.

Bacteria↗

Geology and elevation shape bacterial assembly in Antarctic endolithic communities

Ice free areas of continental Antarctica are among the coldest and driest environments on Earth, and yet, they support surprisingly diverse and highly adapted microbial communities. Endolithic growth is one of the key adaptations to such extreme environments and often represents the dominant life-form. Despite growing scientific interest, little is known of the mechanisms that influence the assembly of endolithic microbiomes across these harsh environments. Here, we used metagenomics to examine the diversity and assembly of endolithic bacterial communities across Antarctica within different rock types and over a large elevation range. While granite supported richer and more heterogeneous communities than sandstone, elevation had no apparent effect on taxonomic richness, regardless of rock type. Conversely, elevation was clearly associated with turnover in community composition, with the deterministic process of variable selection driving microbial assembly along the elevation gradient. The turnover associated with elevation was modulated by geology, whereby for a given elevation difference, turnover was consistently larger between communities inhabiting different rock types. Overall, selection imposed by elevation and geology appeared stronger than turnover related to other spatially-structured environmental drivers. Our findings indicate that at the cold-arid limit of life on Earth, geology and elevation are key determinants of endolithic bacterial heterogeneity. This also suggests that warming temperatures may threaten the persistence of such extreme-adapted organisms.

54 ENVIRONMENTAL SCIENCES↗

Global Diversity and Biogeography of the Zostera marina Mycobiome

Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens, or endophytes in global ecosystems. Here, we characterize the distribution of fungi associated with the seagrass Zostera marina, using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S rRNA gene, we first measured fungal community composition and diversity. We then tested hypotheses of neutral community assembly theory and the degree to which deviations suggested that amplicon sequence variants (ASVs) were plant selected or dispersal limited. Finally, we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. We found that the fungal community is significantly different between sites and that the leaf mycobiome follows a weak but significant pattern of distance decay in the Pacific Ocean. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome, with most taxa assembling through stochastic processes. The Z. marina core leaf and root mycobiomes were dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp., and Saccharomyces sp. It is clear from the many unclassified fungal ASVs and fungal functional guilds that knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses. Fungi have important functional roles when associated with land plants, yet very little is known about the roles of fungi associated with marine plants, like seagrasses. In this study, we report the results of a global effort to characterize the fungi associated with the seagrass Zostera marina across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases that general knowledge of seagrass-associated fungi and marine fungi is lacking. This work serves as an important foundational step toward future work investigating the functional ramifications of fungi in the marine ecosystem.

ITS2↗

Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

The processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H 2 production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management.

59 BASIC BIOLOGICAL SCIENCES↗

Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput Fluidigm TM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N 2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. As a result, this research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.

54 ENVIRONMENTAL SCIENCES↗

Characterizing Absolute Orientations in DNA Self-Assembly of Single Molecules

DNA self-assembly of single molecules (i.e., dyes) with deterministic orientations is a powerful approach for engineering mo-lecular excitons. However, current determination methods of the dye orientation relative to DNA do not account for the orien-tation of the dye plane, which is a missing degree of freedom needed to define absolute three-dimensional orientations. In this work, we combine fluorescence-detected linear dichroism, defocused dipole imaging, and DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution microscopy to determine the absolute three-dimensional orientations of single Cy5 dyes relative to host DNA duplexes which includes the dye plane orientation. The data revealed that the absorption and emission dipoles are perpendicular to the DNA duplex, and the mean dye plane is parallel to the DNA bases, which supports the notion that Cy5 dyes intercalate between DNA base pairs. The presented methodology will inspire the investigation of the dye plane orientation for controlling dye arrangement configurations beyond spontaneous π-stacking between dyes as well as achieving novel dye-DNA arrangements.

36 MATERIALS SCIENCE↗

Glycoside Hydrolases across Environmental Microbial Communities

Across many environments microbial glycoside hydrolases support the enzymatic processing of carbohydrates, a critical function in many ecosystems. Little is known about how the microbial composition of a community and the potential for carbohydrate processing relate to each other. Here, using 1,934 metagenomic datasets, we linked changes in community composition to variation of potential for carbohydrate processing across environments. We were able to show that each ecosystem-type displays a specific potential for carbohydrate utilization. Most of this potential was associated with just 77 bacterial genera. The GH content in bacterial genera is best described by their taxonomic affiliation. Across metagenomes, fluctuations of the microbial community structure and GH potential for carbohydrate utilization were correlated. Our analysis reveals that both deterministic and stochastic processes contribute to the assembly of complex microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

Transuranic Transmutation and Criticality Calculation Sensitivity to Heterogeneous Lattice Effects - 12391

Using Mixed Oxide (MOX) fuel in traditional Pressurized Water Reactor (PWR) assemblies has been researched at length and has shown to provide the benefit of transmutation and targets the amount and toxicity of high level waste needed to be managed. Advanced MOX concepts using enriched Uranium Dioxide (UO{sub 2}) are required for multiple recycling of plutonium. The use of MOX and ordinary UO{sub 2} fuel in the same assembly as well as unfueled rods and assembly edge effects contrasts with the unit cell computational assumption of a uniform infinite array of rods. While a deterministic method of calculating the Dancoff factor has traditionally been employed in fuel assembly analysis due to the lighter computational and modeling requirements, this research seeks to determine the validity of the uniform, infinite lattice assumption with respect to Dancoff factor and determine the magnitude of the impact of nonuniform lattice effects on fuel assembly criticality calculations as well as transuranic isotope production and transmutation. This research explored the pin-to-pin interaction in a non-uniform lattice of MOX fuel rods and UO{sub 2} fuel rods through the impact of the calculated Dancoff factors from the deterministic method used in SCALE versus the Monte Carlo method used in the code DANCOFF-MC. Using the Monte Carlo method takes into account the non-uniform lattice effects of having neighboring fuel rods with different cross-sectional spectra whereas the Dancoff factor calculated by SCALE assumes a uniform, infinite lattice of one fuel rod type. Differences in eigenvalue calculations as a function of burnup are present between the two methods of Dancoff factor calculation. The percent difference is greatest at low burnup and then becomes smaller throughout the cycle. Differences in the transmutation rate of transuranic isotopes in the MOX fuel are also present between the Dancoff factor calculation methods. The largest difference is in Pu-239, Pu-242, and Am-241 composition whereas U-238, Pu-242, and Pu-238 composition was not changed by taking into account the non-homogenous lattice effects. Heterogeneous lattice effects do change the calculated eigenvalue and transmutation rate in a non-uniform lattice of MOX fuel rods and UO{sub 2} fuel. However, the uncertainty in the ENDF data used by SCALE in these calculations is large enough that the infinite lattice assumption remains valid. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.

54 ENVIRONMENTAL SCIENCES↗

Advances in the computation of the Sjöstrand, Rossi, and Feynman distributions

This study illustrates recent computational advances in the application of the Sjöstrand (area), Rossi, and Feynman methods to estimate the effective multiplication factor of a subcritical system driven by an external neutron source. The methodologies introduced in this study have been validated with the experimental results from the KUKA facility of Japan by Monte Carlo (MCNP6 and MCNPX) and deterministic (ERANOS, VARIANT, and PARTISN) codes. When the assembly is driven by a pulsed neutron source generated by a particle accelerator and delayed neutrons are at equilibrium, the Sjöstrand method becomes extremely fast if the integral of the reaction rate from a single pulse is split into two parts. These two integrals distinguish between the neutron counts during and after the pulse period. To conclude, when the facility is driven by a spontaneous fission neutron source, the timestamps of the detector neutron counts can be obtained up to the nanosecond precision using MCNP6, which allows obtaining the Rossi and Feynman distributions.

97 MATHEMATICS AND COMPUTING↗

Hybrid Gamma Emission Tomography for the Verification of Unirradiated Fuel: A Viability Study

Current International Atomic Energy Agency (IAEA) methodologies for the verification of fresh low-enriched uranium (LEU) and mixed oxide (MOX) fuel assemblies are volume-averaging methods that lack sensitivity to individual pins. Further, as unirradiated fuel assemblies become more and more complex (e.g., heavy gadolinium loading, high degrees of axial and radial variation in fissile concentration), the accuracy of current IAEA instruments degrades and measurement time increases. Particularly in light of the fact that no special tooling is required to remove individual pins from modern fuel assemblies, new capabilities for the verification of unirradiated (i.e., fresh LEU and MOX) assemblies are needed to ensure that fissile material has not been diverted. Passive gamma emission tomography has demonstrated potential to provide pin-level verification of spent fuel, but gamma-ray emission rates from unirradiated fuel emissions are significantly lower, precluding purely passive tomography methods. The work presented here introduces the concept of Hybrid Gamma Emission Tomography (HGET) for verification of unirradiated fuels, in which a neutron source is used to actively interrogate the fuel assembly and the resulting gamma-ray emissions are imaged using tomographic methods to provide pin-level verification of fissile material concentration. This paper describes the status of a viability study on the HGET concept, including: envisioned use-case scenarios and corresponding definitions of fuel assemblies; modeling framework based on Monte Carlo and deterministic transport methods, and its validation; quantitative assessment of candidate HGET signatures with a focus on prompt fission gamma rays and delayed fission gamma rays; a nominal HGETv1 instrument design; candidate HGET-specific tomographic reconstruction methods that fully incorporate declared information; and examples of simulation-based predictions of HGET performance.

Miller, Erin A.↗

Multigroup Transport Equations Derived via Homogeneity and Isotropy Restoration Theory

The multigroup neutron transport calculation at a cell-level or assembly-level is a key step in conventional deterministic reactor analysis. As the computing power grows, it is contemplated that the multigroup transport equation itself be used in whole-core calculation. While the continuous-energy transport equation is derived straightforwardly and rigorously, the multigroup transport equation currently in use involves several approximations during its derivation. Recently, we proposed the Homogeneity and Isotropy Restoration (HIRE) theory in a preliminary form for deriving a multigroup transport equation that maintains angle-independence in the total cross section and homogeneity in the material region (originally each material region is usually homogeneous by design). As a byproduct, only the isotropic scattering term remained, which also relieved the computational burden significantly. In the Homogeneity and Isotropy Restoration (HIRE) theory, we introduced a discontinuity factor in the form of partial current discontinuity factor (PCDF) at the material interface. In this paper, we elaborate on the HIRE theory and apply it to several typical pin-cell problems. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Microbiome assembly in thawing permafrost and its feedbacks to climate

Abstract The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost–climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post‐thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw‐mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well‐suited to thrive in changing environmental conditions. We predict that on a short timescale and following high‐disturbance thaw (e.g., thermokarst), stochasticity dominates post‐thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower‐intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post‐thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.

54 ENVIRONMENTAL SCIENCES↗

2009.1 Revision of the Evaluated Nuclear Data Library (ENDL2009.1)

LLNL’s Computational Nuclear Data and Theory Group have created a 2009.1 revised release of the Evaluated Nuclear Data Library (ENDL2009.1). This library is designed to support LLNL’s current and future nuclear data needs and will be employed in nuclear reactor, nuclear security and stockpile stewardship simulations with ASC codes. The ENDL2009 database was the most complete nuclear database for Monte Carlo and deterministic transport of neutrons and charged particles. It was assembled with strong support from the ASC PEM and Attribution programs, leveraged with support from Campaign 4 and the DOE/Office of Science’s US Nuclear Data Program. This document lists the revisions and fixes made in a new release called ENDL2009.1, by comparing with the existing data in the original release which is now called ENDL2009.0. These changes are made in conjunction with the revisions for ENDL2011.1, so that both the .1 releases are as free as possible of known defects.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

2009.3 Revision of the Evaluated Nuclear Data Library (ENDL2009.3)

LLNL's Computational Nuclear Data and Theory Group have created a 2009.3 revised release of the Evaluated Nuclear Data Library (ENDL2009.3). This library is designed to support LLNL's current and future nuclear data needs and will be employed in nuclear reactor, nuclear security and stockpile stewardship simulations with ASC codes. The ENDL2009 database was the most complete nuclear database for Monte Carlo and deterministic transport of neutrons and charged particles. It was assembled with strong support from the ASC PEM and Attribution programs, leveraged with support from Campaign 4 and the DOE/Office of Science's US Nuclear Data Program. This document lists the revisions and fixes made in a new release called ENDL2009.3, by com- paring with the existing data in the previous release ENDL2009.2. These changes are made in conjunction with the revisions for ENDL2011.3, so that both the .3 releases are as free as possible of known defects.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗