Whole-genome sequencing of Beauveria bassiana KNU-101 using the hybrid assembly approach.

In this report, we present the whole-genome sequences of Beauveria bassiana KNU-101, a widely recognized entomopathogenic fungus used as a biopesticide. The genome was assembled using a hybrid assembly approach, resulting in 13 scaffolds with a total size of 35,638,224 bp.

Spinach (Spinacia oleracea) as green manure modifies the soil nutrients and microbiota structure for enhanced pepper productivity.

Spinach has been suggested as a potential rotation crop for increasing crop yield by enhancing beneficial fungal microbes in continuous monocropping. However, no research on the use of spinach as a green manure has been reported. Thus, we tested the effects of spinach and Korean mustard cultivars (green and red mustards) (10 g pot -1) as green manure on soil chemical properties, pepper productivity, and soil microbiome of long-year pepper-monocropped soil. Spinach improved the soil nutrition (e.g., pH, SOM, TN, NH4+, and K), weed suppression, and pepper growth. Spinach had by far the highest fruit yield, over 100% pepper fruit yield increment over the mustard green manures and control. Our study showed that the major influencing factors to cause a shift in both bacterial and fungal community assemblies were soil pH, TC TN, and K. Following green manure amendment Bacillota, especially Clostridium, Bacillus and Sedimentibacter, were enriched, whereas Chloroflexi and Acidobacteriota were reduced. In addition, spinach highly reduced the abundance of Leotiomycetes and Fusarium but enriched Papiliotrema. FAPROTAX and FUNGuild analysis revealed that predicted functional profiles of bacterial and fungal communities in spinach-amended soil were changed. Spinach-treated soil was differentially abundant in function related to hydrocarbon degradation and functional guilds of symbiotrophs and ectomycorrhizal. This study contributes significantly to our understanding of how the soil fertility and soil microbiome alteration via spinach green manure application as a pre-plant soil treatment might help alleviate continuous cropping obstacles.

Changes in Microbial Community Structure in Response to Gummosis in Peach Tree Bark.

Peach gummosis disease has been identified as a serious challenge in Korean agriculture and has developed to become a major cause of agricultural productivity losses. However, treatments for gummosis have not been systemically established and studies of the microbiome closely related to this plant disease are lacking. Therefore, we analyzed the bacterial and fungal communities in the bark and rhizosphere soil of healthy peach trees and those with gummosis. Through high-throughput sequencing, we obtained unprecedented insights into the bacterial and fungal dynamics of each group, including their diversity and taxonomic classification, as well as network analyses. We found that the presence of gummosis drives a significantly higher alpha diversity in the bark bacterial community. Peach gummosis bark mycobiomes included greater numbers of opportunistic pathogens such as Ascochyta, Botryosphaeria, Saccharomyces, Nectriaceae_NA, Trametes, and Valsaceae_NA. However, the microbiome also included bacteria beneficial to plant growth and the production of polysaccharides-namely, 1174-901-12, Catenibacterium, Cutibacterium, Friedmanniella, Methylobacterium-Methylorubrum, Pseudomonas, Rhodobacter, and Sphingomonas. Furthermore, we confirmed that gummosis induced a more complex structure in the bark microbiome network. We conclude that the findings of this study provide a valuable aid in profiling the overall peach tree microbial ecosystem, which can be utilized to develop precise biomarkers for the early diagnosis of gummosis.

Complete Genome Sequence of Bacillus amyloliquefaciens KNU-28 Isolated from Peach Leaves (Prunus Persica [L.] Batsch).

This study presented the complete genome sequence of B. amyloliquefaciens KNU-28 isolated from the leaves of the peach (Prunus persica [L.] Batsch). The genome of this strain comprised one chromosome with 4,238,926 bp and 45.9% of GC content.

Pore-scale observations of natural hydrate-bearing sediments via pressure core sub-coring and micro-CT scanning.

Both intra-pore hydrate morphology and inter-pore hydrate distribution influence the physical properties of hydrate-bearing sediments, yet there has been no pore-scale observations of hydrate habit under pressure in preserved pressure core samples so far. We present for the first time a pore-scale micro-CT study of natural hydrate-bearing cores that were acquired from Green Canyon Block 955 in UT-GOM2-1 Expedition and preserved within hydrate pressure-temperature stability conditions throughout sub-sampling and imaging processes. Measured hydrate saturation in the sub-samples, taken from units expected to have in-situ saturation of 80% or more, ranges from 3 ± 1% to 56 ± 11% as interpreted from micro-CT images. Pore-scale observations of gas hydrate in the sub-samples suggest that hydrate in silty sediments at the Gulf of Mexico is pore-invasive rather than particle displacive, and hydrate particles in these natural water-saturated samples are pore-filling with no evidence of grain-coating. Hydrate can form a connected 3D network and provide mechanical support for the sediments even without cementation. The technical breakthrough to directly visualize particle-level hydrate pore habits in natural sediments reported here sheds light on future investigations of pressure- and temperature-sensitive processes including hydrate-bearing sediments, dissolved gases, and other biochemical processes in the deep-sea environment.

Alteration of the Soil Microbiota in Ginseng Rusty Roots: Application of Machine Learning Algorithm to Explore Potential Biomarkers for Diagnostic and Predictive Analytics.

Conceptualization to utilize microbial composition as a prediction tool has been widely applied in human cohorts, yet the potential capacity of soil microbiota as a diagnostic tool to predict plant phenotype remains unknown. Here, we collected 130 soil samples which are 54 healthy controls and 76 ginseng rusty roots (GRRs). Alpha diversities including Shannon, Simpson, Chao1, and phylogenetic diversity were significantly decreased in GRR (P < 0.05). Moreover, we identified 30 potential biomarkers. The optimized markers were obtained through fivefold cross-validation on a support vector machine and yielded a robust area under the curve of 0.856. Notably, evaluation of multi-index classification performance including accuracy, F1-score, and Kappa coefficient also showed robust discriminative capability (90.99%, 0.903, and 0.808). Taken together, our results suggest that the disease affects the microbial community and offers the potential ability of soil microbiota to identifying farms at the risk of GRR.

Effect of Fluid-Rock Interactions on In Situ Bacterial Alteration of Interfacial Properties and Wettability of CO2-Brine-Mineral Systems for Geologic Carbon Storage.

This study explored the feasibility of biosurfactant amendment in modifying the interfacial characteristics of carbon dioxide (CO2) with rock minerals under high-pressure conditions for GCS. In particular, while varying the CO2 phase and the rock mineral, we quantitatively examined the production of biosurfactants by Bacillus subtilis and their effects on interfacial tension (IFT) and wettability in CO2-brine-mineral systems. The results demonstrated that surfactin produced by B. subtilis caused the reduction of CO2-brine IFT and modified the wettability of both quartz and calcite minerals to be more CO2-wet. The production yield of surfactin was substantially greater with the calcite mineral than with the quartz mineral. The calcite played the role of a pH buffer, consistently maintaining the brine pH above 6. By contrast, an acidic condition in CO2-brine-quartz systems caused the precipitation of surfactin, and hence surfactin lost its ability as a surface-active agent. Meanwhile, the CO2-driven mineral dissolution and precipitation in CO2-brine-calcite systems under a non-equilibrium system altered the solid substrates, produced surface roughness, and caused contact angle variations. These results provide unique experimental data on biosurfactant-mediated interfacial properties and wettability in GCS-relevant conditions, which support the exploitation of in situ biosurfactant production for biosurfactant-aided CO2 injection.

Strain behavior of malaligned cervical spine implanted with metal-on-polyethylene, metal-on-metal, and elastomeric artificial disc prostheses - A finite element analysis.

BACKGROUND: Postoperative alterations in cervical spine curvature (i.e. loss of lordotic angle) are frequently observed following total disc replacement surgery. However, it remains unclear whether such changes in lordotic angle are due to preoperative spinal deformities and/or prostheses design limitations. The objective of the study is to investigate strain and segmental biomechanics of the malaligned cervical spine following total disc replacement. METHODS: Three disc prostheses were chosen, namely a metal-on-polyethylene, a metal-on-metal, and an elastomeric prosthesis, which feature different geometrical and material design characteristics. All discs were modelled and implanted into multi-segmental cervical spine finite element model (C3-C7) with normal, straight and kyphotic alignments. Comparative analyses were performed by using a hybrid protocol. FINDINGS: The results indicated that as the spine loses lordotic alignment, the prosthesis with elastomeric core tends to produce significantly larger flexion range of motion (difference up to 6.1°) than metal-on-polyethylene and metal-on-metal prostheses. In contrast, when the treated spine had normal lordotic alignment, the range of motion behaviors of different prostheses are rather similar (difference within 1.9°). Large localized strains up to 84.8% were found with the elastomeric prosthesis, causing a collapsed anterior disc space under flexion loads. INTERPRETATION: Changes in cervical spinal alignments could significantly affect the surgical-level range of motion behaviors following disc arthroplasty; the in situ performance was largely dependent on the designs of the artificial disc devices in particular to the material properties.

Effect of Electric Field on Gas Hydrate Nucleation Kinetics: Evidence for the Enhanced Kinetics of Hydrate Nucleation by Negatively Charged Clay Surfaces.

Natural gas hydrates are found widely in oceanic clay-rich sediments, where clay-water interactions have a profound effect on the formation behavior of gas hydrates. However, it remains unclear why and how natural gas hydrates are formed in clay-rich sediments in spite of factors that limit gas hydrate formation, such as small pore size and high salinity. Herein, we show that polarized water molecules on clay surfaces clearly promote gas hydrate nucleation kinetics. When water molecules were polarized with an electric field of 104 V/m, gas hydrate nucleation occurred significantly faster with an induction time reduced by 5.8 times. Further, the presence of strongly polarized water layers at the water-gas interface hindered gas uptake and thus hydrate formation, when the electric field was applied prior to gas dissolution. Our findings expand our understanding of the formation habits of naturally occurring gas hydrates in clay-rich sedimentary deposits and provide insights into gas production from natural hydrate deposits.

Characterization of Quadratic Nonlinearity between Motion Artifact and Acceleration Data and its Application to Heartbeat Rate Estimation.

Accelerometers are applied to various applications to collect information about movements of other sensors deployed at diverse fields ranging from underwater area to human body. In this study, we try to characterize the nonlinear relationship between motion artifact and acceleration data. The cross bicoherence test and the Volterra filter are used as the approaches to detection and modeling. We use the cross bicoherence test to directly detect in the frequency domain and we indirectly identify the nonlinear relationship by improving the performance of eliminating motion artifact in heartbeat rate estimation using a nonlinear filter, the second-order Volterra filter. In the experiments, significant bicoherence values are observed through the cross bicoherence test between the photoplethysmogram (PPG) signal contaminated with motion artifact and the acceleration sensor data. It is observed that for each dataset, the heartbeat rate estimation based on the Volterra filter is superior to that of the linear filter in terms of average absolute error. Furthermore, the leave one out cross-validation (LOOCV) is employed to develop an optimal structure of the Volterra filter for the total datasets. Due to lack of data, the developed Volterra filter does not demonstrate significant difference from the optimal linear filter in terms of t-test. Through this study, it can be concluded that motion artifact may have a quadaratical relationship with acceleration data in terms of bicoherence and more experimental data are required for developing a robust and efficient model for the relationship.

Biosurfactant as an Enhancer of Geologic Carbon Storage: Microbial Modification of Interfacial Tension and Contact Angle in Carbon dioxide/Water/Quartz Systems.

Injecting and storing of carbon dioxide (CO2) in deep geologic formations is considered as one of the promising approaches for geologic carbon storage. Microbial wettability alteration of injected CO2 is expected to occur naturally by microorganisms indigenous to the geologic formation or microorganisms intentionally introduced to increase CO2 storage capacity in the target reservoirs. The question as to the extent of microbial CO2 wettability alteration under reservoir conditions still warrants further investigation. This study investigated the effect of a lipopeptide biosurfactant-surfactin, on interfacial tension (IFT) reduction and contact angle alteration in CO2/water/quartz systems under a laboratory setup simulating in situ reservoir conditions. The temporal shifts in the IFT and the contact angle among CO2, brine, and quartz were monitored for different CO2 phases (3 MPa, 30°C for gaseous CO2; 10 MPa, 28°C for liquid CO2; 10 MPa, 37°C for supercritical CO2) upon cultivation of Bacillus subtilis strain ATCC6633 with induced surfactin secretion activity. Due to the secreted surfactin, the IFT between CO2 and brine decreased: from 49.5 to 30 mN/m, by ∼39% for gaseous CO2; from 28.5 to 13 mN/m, by 54% for liquid CO2; and from 32.5 to 18.5 mN/m, by ∼43% for supercritical CO2, respectively. The contact angle of a CO2 droplet on a quartz disk in brine increased: from 20.5° to 23.2°, by 1.16 times for gaseous CO2; from 18.4° to 61.8°, by 3.36 times for liquid CO2; and from 35.5° to 47.7°, by 1.34 times for supercritical CO2, respectively. With the microbially altered CO2 wettability, improvement in sweep efficiency of injected and displaced CO2 was evaluated using 2-D pore network model simulations; again the increment in sweep efficiency was the greatest in liquid CO2 phase due to the largest reduction in capillary factor. This result provides novel insights as to the role of naturally occurring biosurfactants in CO2 storage and suggests that biostimulation of biosurfactant production may be a feasible technique for enhancement of CO2 storage capacity.

Comparison of the Atomic Layer Deposition of Tantalum Oxide Thin Films Using Ta(NtBu)(NEt2)3, Ta(NtBu)(NEt2)2Cp, and H2O.

The growth characteristics of Ta2O5 thin films by atomic layer deposition (ALD) were examined using Ta(NtBu)(NEt2)3 (TBTDET) and Ta(NtBu)(NEt2)2Cp (TBDETCp) as Ta-precursors, where tBu, Et, and Cp represent tert-butyl, ethyl, and cyclopentadienyl groups, respectively, along with water vapor as oxygen source. The grown Ta2O5 films were amorphous with very smooth surface morphology for both the Ta-precursors. The saturated ALD growth rates of Ta2O5 films were 0.77 Å cycle-1 at 250 °C and 0.67 Å cycle-1 at 300 °C using TBTDET and TBDETCp precursors, respectively. The thermal decomposition of the amido ligand (NEt2) limited the ALD process temperature below 275 °C for TBTDET precursor. However, the ALD temperature window could be extended up to 325 °C due to a strong Ta-Cp bond for the TBDETCp precursor. Because of the improved thermal stability of TBDETCp precursor, excellent nonuniformity of ∼2% in 200 mm wafer could be achieved with a step coverage of ∼90% in a deep hole structure (aspect ratio 5:1) which is promising for 3-dimensional architecture to form high density memories. Nonetheless, a rather high concentration (∼7 at. %) of carbon impurities was incorporated into the Ta2O5 film using TBDETCp, which was possibly due to readsorption of dissociated ligands as small organic molecules in the growth of Ta2O5 film by ALD. Despite the presence of high carbon concentration which might be an origin of large leakage current under electric fields, the Ta2O5 film using TBDETCp showed a promising resistive switching performance with an endurance cycle as high as ∼17 500 for resistance switching random access memory application. The optical refractive index of the deposited Ta2O5 films was 2.1-2.2 at 632.8 nm using both the Ta-precursors, and indirect optical band gap was estimated to be ∼4.1 eV for both the cases.

Electrical Characteristics of Metal-Oxide-Semiconductor Capacitor with High-κ/Metal Gate Using Oxygen Scavenging Process.

It has been widely accepted that the mismatch of lattice constants between HfO2 and Si generates interface traps at the HfO2-Si interface, which causes the degradation of device performances. For better interface quality, very thin SiO2 film (< 2 nm) has been inserted as an interlayer (IL) between HfO2 and Si despite of the increase of EOT. In order to obtain both the better interface quality and the reduction of EOT, we used Ti metal on HfO2/IL SiO2 stack as a scavenging layer to absorb oxygens in the SiO2 and various annealing conditions were applied to optimize the thickness of the SiO2. As a result, we can effectively shrink the EOT from 3.55 nm to 1.15 nm while maintaining the same physical thickness of gate stacks. Furthermore, the diffusion of oxygen was confirmed by high resolution transmission electron microscopy (HRTEM) and time-of-flight secondary ion mass Spectrometry (SIMS).

Enhanced reductive dechlorination of tetrachloroethene by nano-sized mackinawite with cyanocobalamin in a highly alkaline condition.

In this study, we characterize the reductive dechlorination of tetrachloroethene (PCE) by nano-sized mackinawite (nFeS) with cobalamin (Cbl(III)) at a high pH and investigate the effects of environmental factors, including the concentrations of the target contaminant, reductant, and catalyst and suspension ions on the dechlorination kinetics of PCE. Ninety five percent of the PCE was degraded by nFeS with Cbl(III) in 15 h. Cyclic voltammetry conducted with regard to the reductive dechlorination showed a higher redox potential of mackinawite under a high-pH condition (-1.01 V), suggesting that the oxidation state of the central cobalt ion in the cobalamin could be reduced to Cbl(I). The change of cobalamin species on the nFeS surface was verified under different pH conditions by UV-vis spectroscopy. The rate constant of PCE dechlorination increased from 0.1582 to 0.4284 h(-1) due to the increase in the nFeS content (2.085-20.85 g/L). As the concentration of Cbl(III) increased from 0 to 0.5 mM, the dechlorination kinetics of PCE was accelerated (0-1.4091 h(-1)) but reached a state of equilibrium from 0.5 to 1 mM. The increase in the initial PCE concentration (0.035-1.0 mM) slowed down the dechlorination kinetics (0.2036-0.0962 h(-1)). The dechlorination kinetics was enhanced by 1.5-11 times when 10 mM of ions (Na(+), K(+), Mg(2+), Ca(2+), CO3(2-), SO4(2-), and NO3(-)) were added, while an addition of HCO3 decelerated it by 10 times. This study can provide background knowledge pertaining to the PCE dechlorination by a natural reductant under a high-pH condition and the effect of environmental factors on the dechlorination kinetics for the development of novel remediation technologies.

Effect of organic matter on CO(2) hydrate phase equilibrium in phyllosilicate suspensions.

In this study, we examined various CO2 hydrate phase equilibria under diverse, heterogeneous conditions, to provide basic knowledge for successful ocean CO2 sequestration in offshore marine sediments. We investigated the effect of geochemical factors on CO2 hydrate phase equilibrium. The three-phase (liquid-hydrate-vapor) equilibrium of CO2 hydrate in the presence of (i) organic matter (glycine, glucose, and urea), (ii) phyllosilicates [illite, kaolinite, and Na-montmorillonite (Na-MMT)], and (iii) mixtures of them was measured in the ranges of 274.5-277.0 K and 14-22 bar. Organic matter inhibited the phase equilibrium of CO2 hydrate by association with water molecules. The inhibition effect decreased in the order: urea < glycine < glucose. Illite and kaolinite (unexpandable clays) barely affected the CO2 hydrate phase equilibrium, while Na-MMT (expandable clay) affected the phase equilibrium because of its interlayer cations. The CO2 hydrate equilibrium conditions, in the illite and kaolinite suspensions with organic matter, were very similar to those in the aqueous organic matter solutions. However, the equilibrium condition in the Na-MMT suspension with organic matter changed because of reduction of its inhibition effect by intercalated organic matter associated with cations in the Na-MMT interlayer.