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At least 235 records · Page 13

Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche

Abstract Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces. One example is gut mucosal communities, where dense, closely packed communities develop under the concurrent influence of nutrient transport from the lumen and fluid-mediated detachment of bacteria. In this study, we model a mucosal niche through a coupled agent-based and finite-volume modeling approach. This methodology enables us to model bacterial interactions affected by nutrient release from various sources while adjusting individual bacterial kinetics. We explored how the dispersion and abundance of bacteria are influenced by biochemical kinetics in different types of metabolic interactions, with a particular focus on the trade-off between growth rate and yield. Our findings demonstrate that in competitive scenarios, higher growth rates result in a larger share of the niche space. In contrast, growth yield plays a critical role in neutralism, commensalism, and mutualism interactions. When bacteria are introduced sequentially, they cause distinct spatiotemporal effects, such as deeper niche colonization in commensalism and mutualism scenarios driven by species intermixing effects, which are enhanced by high growth yields. Moreover, sub-ecosystem interactions dictate the dynamics of three-species communities, sometimes yielding unexpected outcomes. Competitive, fast-growing bacteria demonstrate robust colonization abilities, yet they face challenges in displacing established mutualistic systems. Bacteria that develop a cooperative relationship with existing species typically obtain niche residence, regardless of their growth rates, although higher growth yields significantly enhance their abundance. Our results underscore the importance of bacterial niche dynamics in shaping community properties and succession, highlighting a new approach to manipulating microbial systems.

Microbiology↗

Observations and Modeling of Fiber-Optics Strain on Hydraulic Fracture Height Growth in HFTS-2

Understanding fracture height growth can be of great significance to optimizing field development and improving recovery. The Hydraulic Fracturing Test Site 2 (HFTS-2) has provided a unique opportunity and an advanced dataset to allow us to observe and understand fracture geometries rigorously. Low frequency distributed acoustic sensing (LF-DAS) data from a vertical well in HFTS-2 showed three key observations: (i) excessive upward height growth (>1000 ft) and limited downward growth of the hydraulic fractures during pumping, (ii) considerable additional upward fracture height growth (~300 ft) after well shut in, and (iii) very complex LF-DAS strain rate patterns for a small fiber-to-stage offset. Advanced geomechanical modeling was performed to simulate the hydraulic fracture propagation and the resulting strain responses in the vertical direction. The modeling results demonstrated asymmetric upward and downward fracture height growths as observed in HFTS-2 with a similar upward height growth rate. Simulated waterfall plots of vertical strain rate showed distinct patterns for different fiber-to-fracture distances. The upward-growing fracture tip can be clearly identified by the interfaces between compressing and extending zones. It was also found that the complex strain rate patterns observed in HFTS-2 for small fiber-stage offsets were not caused by the mechanical layering but possibly result from the simultaneous propagation of multiple hydraulic fractures at different rates. Furthermore, the simulation results improved the understating of the HFTS-2 LF-DAS data and the simulated strain rate patterns could also serve as templates for fracture height interpretation from LF-DAS data in future.

58 GEOSCIENCES↗

Phase-field modeling of orientation-dependent crack growth in ductile single crystals with anisotropic elasticity

Crack growth in ductile single crystals (DuSCs) is orientation dependent due to the anisotropies of crystal plasticity and elastic tensor. This study develops a phase-field model incorporating both crystal plasticity and crack growth and proposes a general method to decompose the elastic energy into compressive and tensile parts to prevent crack growth under compression in the phase-field description. The phase-field model, in combination with three Euler angles, is employed to simulate orientation-dependent crack growth in DuSCs. The contributions from crystal plasticity and anisotropic elasticity are compared, and the former is found to dominate in the anisotropy of crack growth in copper single crystals. Furthermore, the simulation results demonstrate that crystal orientation strongly affects the heterogeneous distribution of plastic strain and the interaction between plastic strain and crack growth. High-throughput phase-field simulations are performed with exhaustive crystal orientations, and the results are explained based on the anisotropy of the Taylor factor.

Computational Solid Mechanics↗

Observations and Modeling of Fiber Optic Strain on Hydraulic Fracture Height Growth in Hydraulic Fracturing Test Site 2 (HFTS-2)

Summary Understanding fracture height growth can be of great significance to optimizing field development and improving recovery. The Hydraulic Fracturing Test Site 2 (HFTS-2) has provided a unique opportunity and an advanced data set to allow us to observe and understand fracture geometries rigorously. Low-frequency distributed acoustic sensing (LF-DAS) data from a vertical well in HFTS-2 showed three key observations: (i) excessive upward height growth (>1,000 ft) and limited downward growth of the hydraulic fractures during pumping, (ii) considerable additional upward fracture height growth (~300 ft) after well shut in, and (iii) very complex LF-DAS strain rate patterns for a small fiber-to-stage offset. Advanced geomechanical modeling was performed to simulate the hydraulic fracture propagation and the resulting strain responses in the vertical direction. The modeling results demonstrated asymmetric upward and downward fracture height growths as observed in HFTS-2 with a similar upward height growth rate. Simulated waterfall plots of vertical strain rate showed distinct patterns for different fiber-to-fracture distances. The upward-growing fracture tip can be clearly identified by the interfaces between compressing and extending zones. It was also found that the complex strain rate patterns observed in HFTS-2 for small fiber-stage offsets were not caused by the mechanical layering but possibly result from the simultaneous propagation of multiple hydraulic fractures at different rates. The simulation results improved the understating of the HFTS-2 LF-DAS data, and the simulated strain rate patterns could also serve as templates for fracture height interpretation from LF-DAS data in future.

Engineering↗

Removal of primary nutrient degrading members severely reduces growth of soil microbial communities even when additional degraders are present

Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here we used a model substrate, chitin, and a Model Soil Consortium, MSC-2, to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent. To characterize specific roles within this representative community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members. Our results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed as well as alterations in the metabolic profile, especially when Streptomyces was removed. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration. Our findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.

McClure, Ryan S↗

Removal of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancy

Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here, we used a model substrate, chitin, and a synthetic Model Soil Consortium (MSC-2) to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent. To characterize specific roles within this synthetic community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO 2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members. Our results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed, as well as alterations in the metabolic profile, especially when Streptomyces was lacking. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration. Our findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.

59 BASIC BIOLOGICAL SCIENCES↗

Methods and apparatus for gnotobiotic plant growth

The disclosure relates to a plant growth apparatus and related system to grow and maintain plants under controlled biotic conditions, for example to grow axenic (microbe-free) plants, gnotobiotic (defined microbiota) plants, and holoxenic (complex, or undefined microbiota) plants. This system allows aseptic bottom irrigation with water, soluble nutrients, chemicals, and/or microbiota. Plants can be inverted for dipping and/or vacuum infiltration. The system also allows for passive (gravity) drainage, thereby allowing for gas exchange and preventing root anoxia. A variety of plant growth substrates can be used within the plant growth apparatus as a plant growth medium. The plant growth apparatus, containing the growth substrate medium, can be completely flushed via the drainage port to remove potential toxic byproducts of the sterilization processes. The entire system is suitably constructed using autoclavable material.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamics and growth rate implications of ribosomes and mRNAs interaction in E. coli

Understanding how cells grow and adapt under various nutrient conditions is pivotal in the study of biological stoichiometry. Recent studies provide empirical evidence that cells use multiple strategies to maintain an optimal protein production rate under different nutrient conditions. Mathematical models can provide a solid theoretical foundation that can explain experimental observations and generate testable hypotheses to further our understanding of the growth process. In this study, we generalize a modeling framework that centers on the translation process and study its asymptotic behaviors to validate algebraic manipulations involving the steady states. Using experimental results on the growth of E. coli under C-, N-, and P-limited environments, we simulate the expected quantitative measurements to show the feasibility of using the model to explain empirical evidence. Our results support the findings that cells employ multiple strategies to maintain a similar protein production rate across different nutrient limitations. Moreover, we find that the previous study underestimates the significance of certain biological rates, such as the binding rate of ribosomes to mRNA and the transition rate between different ribosomal stages. Furthermore, our simulation shows that the strategies used by cells under C- and P-limitations result in a faster overall growth dynamics than under N-limitation. In conclusion, the general modeling framework provides a valuable platform to study cell growth under different nutrient supply conditions, which also allows straightforward extensions to the coupling of transcription, translation, and energetics to deepen our understanding of the growth process.

59 BASIC BIOLOGICAL SCIENCES↗

Mass spectral imaging showing the plant growth-promoting rhizobacteria's effect on the Brachypodium awn

The plant growth-promoting rhizobacteria (PGPR) on the host plant surface play a key role in biological control and pathogenic response in plant functions and growth. However, it is difficult to elucidate the PGPR effect on plants. Such information is important in biomass production and conversion. Brachypodium distachyon (Brachypodium), a genomics model for bioenergy and native grasses, was selected as a C3 plant model; and the Gram-negative Pseudomonas fluorescens SBW25 ( P.) and Gram-positive Arthrobacter chlorophenolicus A6 ( A.) were chosen as representative PGPR strains. The PGPRs were introduced to the Brachypodium seed's awn prior to germination, and their possible effects on the seeding and growth were studied using different modes of time-of-flight secondary ion mass spectrometry (ToF-SIMS) measurements, including a high mass-resolution spectral collection and delayed image extraction. We observed key plant metabolic products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and auxin indole-3-acetic acid in the Brachypodium awns. Furthermore, principal component analysis and two-dimensional imaging analysis reveal that the Brachypodium awns are sensitive to the PGPR, leading to chemical composition and morphology changes on the awn surface. Our results show that ToF-SIMS can be an effective tool to probe cell-to-cell interactions at the biointerface. This work provides a new approach to studying the PGPR effects on awn and shows its potential for the research of plant growth in the future.

metabolite↗

Decoding anomalous grain growth at room temperature during pressure-induced phase transformations

Significant grain growth is observed during the high-pressure phase transformations (PTs) at room temperature in various materials. The main focus here is grain growth from a few hundred nanometers to 10 μm within an hour during α → ω PT in Zr. No existing theory explains this phenomenon since without PT, Zr nanocrystals do not grow at room temperature even for up to 10 years. Here, in this study, a multistep mechanism for the grain growth during α → ω PT in Zr is suggested. Phase interfaces (PI) and grain boundaries (GBs) coincide and move together as a combined PI-GBs under the action of the combined thermodynamic driving force. Such a combined motion changes the diffusional grain growth mechanism to the transformational one and the martensitic mechanism of PT to a reconstructive one via an intermediate disordered phase. The primary condition is that the GB energy of the ω phase is smaller than that of the α phase, which promotes the nucleation of ω-Zr and is consistent with the absence of the reverse PT and reduction in the PT pressure with reducing grain size. Several intermediate steps for such motion are suggested and justified kinetically. Nonhydrostatic stresses due to volume reduction in the growing ω grain promote continuous growth of the existing ω grain instead of a new nucleation at other GBs. In situ synchrotron Laue diffraction experiments confirm the main predictions of the theory. The suggested mechanism provides a new insight into synergistic interaction between PTs and microstructure evolution.

anomalous grain growth during phase transformation↗

Vapor transport growth of MnBi 2 Te 4 and related compounds

Motivated by fine tuning of the magnetic and topological properties of MnBi 2 Te 4 via defect engineering, in this work, we report the crystal growth of MnBi 2 Te 4 and related compounds using vapor transport method and crystal characterization by measuring elemental ratio, magnetic and transport properties, and scanning tunneling microscopy. For the growth of MnBi 2 Te 4 single crystals, I 2 , MnI 2 , MnCl 2 , TeCl 4 , and MoCl 5 are all effective transport agents; chemical transportation occurs faster in the presence of iodides than chlorides. We further successfully grow MnSb 2 Te 4 , MnBi 2-x Sb x Te 4 , and Sb-doped MnBi 4 Te 7 crystals. A small temperature gradient< 20°C between the hot and cold ends of the growth ampoule is critical for the successful crystal growth of MnBi 2 Te 4 and related compounds. Compared to flux grown crystals, vapor transported crystals tend to be Mn stoichiometric, and Sb-bearing compositions have more Mn/Sb site mixing. The vapor transport growth provides a new materials synthesis approach to fine tune the magnetic and topological properties of these intrinsic magnetic topological insulators where controlling defects is vital.

36 MATERIALS SCIENCE↗

Single crystal growth and characterization of topological semimetal ZrSnTe

High quality single crystals are critical for experimental materials science research. ZrSnTe represents such an example. This material belongs to the ZrSiS-type topological material family, which is so far the only one in this material family possessing Fermi surface formed by Dirac bands generated by a Sn-square net. Experimental study on ZrSnTe is limited due to the difficulty in single crystal growth. Here, in this work, we report the single crystal growth for ZrSnTe using a solid-state reaction method with Sn as a flux. The roles of various growth parameters such as the molar ratio of starting materials, growth temperature and cooling rate in obtaining sizeable single crystals were investigated. The quality of the obtained single crystals was checked by elemental, structural and electronic characterizations. Our study on the growth method for ZrSnTe would enable the future study on this less explored topological semimetal.

36 MATERIALS SCIENCE↗

Unveiling the nucleation and growth of Zr oxide precipitates in internally oxidized Nb3Sn superconductors

We report on atomic-scale analyses of nucleation and growth of Zr oxide precipitates and the microstructural evolution of internally oxidized Nb3Sn wires for high-field superconducting magnet applications, utilizing atom probe tomography (APT), transmission electron microscopy (TEM), and first-principles calculations. APT analyses reveal that oxygen and zirconium are already segregated at grain boundaries (GBs) in the unreacted Nb-1Zr-4Ta (at%) alloy prior to forming Nb3Sn through reacting the Nb alloy with Sn and SnO2. After forming Nb3Sn, Zr oxide precipitates nucleate both at the Nb3Sn/Nb heterophase interfaces and in the Nb3Sn grains, driven by the small solubilities of Zr and O in Nb3Sn compared to their value in Nb. A high number density (Nv) of Zr oxide nanoprecipitates is observed in the Nb3Sn layers, ∼10 23 m −3 , with a mean diameter <10 nm for a heat treatment at 625 °C. Quantitative APT and TEM analyses of the Zr oxide precipitates in the reacted Nb3Sn layers elucidate details of the nucleation, growth, and coarsening processes of the Zr oxide precipitates in Nb3Sn. First-principles calculations and classical nucleation theory are employed to study the nucleation of Zr oxide precipitates in Nb3Sn and to estimate the maximum energy barrier and critical radius for nucleation. Our research unveils the kinetic pathways for nucleation and growth of Zr oxide precipitates and the microstructural evolution of Nb3Sn layers, which helps to understand and improve the superconducting properties of internally oxidized Nb3Sn wires for use in high-field superconducting magnets. •We investigated the nucleation and growth of Zr oxide nanoprecipitates in Nb3Sn superconductors for magnet applications.•APT and TEM analyses reveals the nucleation and growth process of Zr oxide precipitates in Nb3Sn layers.•Classical nucleation theory with DFT is employed to describe the nucleation process of Zr oxide precipitates in Nb3Sn.•We find that the interfacial reactions at Nb/Nb3Sn interface play a critical role in the nucleation of Zr oxide precipitates.•Current study provides a pathway to improve the properties of internally oxidized Nb3Sn superconducting wires.

43 PARTICLE ACCELERATORS↗

Tailoring grain growth and solid solution strengthening of single-phase CrCoNi medium-entropy alloys by solute selection

In the present study, we selected solutes to be added to the CrCoNi medium-entropy alloy (MEA) based on the mismatch of self-diffusion activation energy (SDQ) between the alloying elements and constituent elements of the matrix, and then investigated their grain growth behavior and mechanical properties. Mo and Al were selected as the solutes for investigation primarily because they have higher and lower SDQ, respectively, than those of the matrix elements; a secondary factor was their higher and lower shear modulus. Their concentrations were fixed at 3 at.% each because previous work had shown these compositions to be single-phase solid solutions with the face-centered cubic structure. Three alloys were produced by arc melting, casting, homogenizing, cold rolling and annealing at various temperatures and times to produce samples with different grain sizes. They were (a) the base alloy CrCoNi, (b) the base alloy plus 3 at.% Mo, and (c) the base alloy plus 3 at.% Al. The activation energies for grain growth of the CrCoNi, CrCoNi-3Mo and CrCoNi-3Al MEAs were found to be ~251, ~368 and ~219 kJ/mol, respectively, consistent with the notion that elements with higher SDQ (in this study Mo) retard grain growth (likely by a solute-drag effect), whereas those with lower values (Al) accelerate grain growth. The room-temperature tensile properties show that Mo increases the yield strength by ~40% but Al addition has a smaller strengthening effect consistent with their relative shear moduli. The yield strength as a function of grain size for the three singlephase MEAs follows the classical Hall-Petch relationship with much higher slopes (> 600 MPa μm -0.5 ) than traditional solid solutions. Furthermore, this work shows that the grain growth kinetics and solid solution strengthening of the CrCoNi MEA can be tuned by selecting solute elements that have appropriate diffusion and physical properties.

36 MATERIALS SCIENCE↗

Ion redistributions at interfaces facilitate nucleation and growth of branched Ag 3 PO 4 polypods

Branched structures are of spectacular interest due to their improved light-harvesting, direct carrier transportation pathway, high surface area, and controllable electronic structures. Understanding their growth mechanisms and controlling factors enables the design of materials with improved functions. Interfaces of liquid-solid and air-liquid are known to change the chemical and physical properties of the liquid solution. However, their role in crystal growth, especially of branched structures, is seldom investigated. In this work we synthesized branched silver phosphate polypods in a thin layer of aqueous solution at room temperature taking advantage of the unique properties near the interfaces. The branched crystals nucleate and grow with a liquid thickness of 810 µm or below requiring the presence of both the gas-liquid and liquid-solid interfaces. The hydrophilicity of the solid substrate also facilitates nucleation and growth. Our results indicate that the synergism of long-range electric fields (ion distributions) at the interfaces promotes not only the nucleation and growth of silver phosphate but also the formation of branched structures. This work can be a reference for facilitating crystal nucleation and growth and controlling structures with specific morphologies, such as branched ones, by understanding and mimicking the properties at the interfaces.

36 MATERIALS SCIENCE↗

Controlling circuitry underlies the growth optimization of Saccharomyces cerevisiae

Microbial growth emerges from coordinated synthesis of various cellular components from limited resources. In Saccharomyces cerevisiae, cyclic AMP (cAMP)-mediated signaling is shown to orchestrate cellular metabolism; however, it remains unclear quantitatively how the controlling circuit drives resource partition and subsequently shapes biomass growth. Here we combined experiment with mathematical modeling to dissect the signaling-mediated growth optimization of S. cerevisiae. We showed that, through cAMP-mediated control, the organism achieves maximal or nearly maximal steady-state growth during the utilization of multiple tested substrates as well as under perturbations impairing glucose uptake. However, the optimal cAMP concentration varies across cases, suggesting that different modes of resource allocation are adopted for varied conditions. Under settings with nutrient alterations, S. cerevisiae tunes its cAMP level to dynamically reprogram itself to realize rapid adaptation. Moreover, to achieve growth maximization, cells employ additional regulatory systems such as the GCN2-mediated amino acid control. This study establishes a systematic understanding of global resource allocation in S. cerevisiae, providing insights into quantitative yeast physiology as well as metabolic strain engineering for biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗

Unveiling the Interfacial Reconstruction Mechanism Enabling Stable Growth of the Delafossite PdCoO 2 on Al 2 O 3 and LaAlO 3

Delafossites, composed of noble metal (A + ) and strongly correlated sublayers (BO 2 – ), form natural superlattices with highly anisotropic properties. These properties hold significant promise for various applications, but their exploitation hinges on the successful growth of high-quality thin films on suitable substrates. Unfortunately, the unique lattice geometry of delafossites presents a significant challenge to thin-film fabrication. Different delafossites grow differently, even when deposited on the same substrate, ranging from successful epitaxy to complete growth suppression. These variations often lack a clear correlation to obvious causes like lattice mismatch. Unidentified stabilization mechanisms appear to enable growth in certain cases, allowing these materials to form stable thin films or act as buffer layers for subsequent delafossite growth. This study employs advanced scanning transmission electron microscopy techniques to investigate the nucleation mechanism underlying the stable growth of PdCoO 2 films on Al 2 O 3 and LaAlO 3 substrates grown via molecular-beam epitaxy. Our findings reveal the presence of a secondary phase within the substrate surface that stabilizes the films. This mechanism deviates from the conventional understanding of strain relief mechanisms at oxide heterostructure interfaces and differs significantly from those observed for Cu-based delafossites.

36 MATERIALS SCIENCE↗

In situ x-ray studies of growth of complex oxides on graphene by molecular beam epitaxy

Future technologies are likely to exploit flexible heterostructures exhibiting multifunctional properties constructed from multiple materials. One technique for the synthesis of such systems relies on remote epitaxy, a method employing graphene as a sacrificial layer between a crystalline substrate and an epitaxial film. The technique can be used to create single crystal heterostructures comprised of stacked epitaxial films, their properties optimized by minimizing incompatibilities between the different materials. Details regarding nucleation and growth via remote epitaxy remain unknown, however, due to the many difficulties in studying synthesis in the growth environment with atomic-scale resolution. Here, we describe an in situ synchrotron x-ray investigation of complex oxide thin film growth on graphene by molecular beam epitaxy. Phase retrieval methods were used to reconstruct the electron density profiles from x-ray crystal truncation rods measured under different growth conditions. Our in situ observations combined with post-growth spectroscopy provide a number of key insights regarding graphene in the synthesis environment and the resulting effects on the complex oxide/graphene heterostructure.

36 MATERIALS SCIENCE↗