Pathogenicity and transmissibility of bovine H5N1 influenza virus.

Highly pathogenic H5N1 avian influenza (HPAI H5N1) viruses occasionally infect, but typically do not transmit, in mammals. In the Spring of 2024, an unprecedented outbreak of HPAI H5N1 in bovine herds occurred in the US, with virus spread within and between herds, infections in poultry and cats, and spillover into humans, collectively indicating an increased public health risk1-4. Here, we characterized an HPAI H5N1 virus isolated from infected cow milk in mice and ferrets. Like other HPAI H5N1 viruses, the bovine H5N1 virus spread systemically, including to the mammary glands of both species; however, this tropism was also observed for an older HPAI H5N1 virus isolate. Importantly, bovine HPAI H5N1 virus bound to sialic acids expressed in human upper airways and inefficiently transmitted to exposed ferrets (one of four exposed ferrets seroconverted without virus detection). Bovine HPAI H5N1 virus thus possesses features that may facilitate infection and transmission in mammals.

Matrix lumican endocytosed by immune cells controls receptor ligand trafficking to promote TLR4 and restrict TLR9 in sepsis.

Infections and inflammation are profoundly influenced by the extracellular matrix (ECM), but their molecular underpinnings are ill defined. Here, we demonstrate that lumican, an ECM protein normally associated with collagens, is elevated in sepsis patients' blood, while lumican-null mice resolve polymicrobial sepsis poorly, with reduced bacterial clearance and greater body weight loss. Secreted by activated fibroblasts, lumican promotes Toll-like receptor (TLR) 4 response to bacterial lipopolysaccharides (LPS) but restricts nucleic acid-specific TLR9 in macrophages and dendritic cells. The underlying mechanism involves lumican attachment to the common TLR coreceptor CD14 and caveolin 1 (Cav1) in lipid rafts on immune cell surfaces via two epitopes, which may be cryptic in collagen-associated lumican. The Cav1 binding epitope alone is sufficient for cell surface enrichment of Cav1, while both are required for lumican to increase cell surface TLR4, CD14, and proinflammatory cytokines in response to LPS. Endocytosed lumican colocalizes with TLR4 and LPS and promotes endosomal induction of type I interferons. Lumican-null macrophages show elevated TLR9 in signal-permissive endolysosomes and increased response, while wild types show lumican colocalization with CpG DNA but not TLR9, consistent with a ligand sequestering, restrictive role for lumican in TLR9 signaling. In vitro, lumican competes with CD14 to bind CpG DNA; biglycan, a lumican paralog, also binds CpG DNA and suppresses TLR9 response. Thus, lumican and other ECM proteins, synthesized de novo or released from collagen association during ECM remodeling, may be internalized by immune cells to regulate their transcriptional programs and effector responses that may be harnessed in future therapeutics.

Evaluating the Soil Quality Index Using Three Methods to Assess Soil Fertility.

Soil health plays a crucial role in crop production, both in terms of quality and quantity, highlighting the importance of effective methods for preserving soil quality to ensure global food security. Soil quality indices (SQIs) have been widely utilized as comprehensive measures of soil function by integrating multiple physical, chemical, and biological soil properties. Traditional SQI analysis involves laborious and costly laboratory analyses, which limits its practicality. To overcome this limitation, our study explores the use of visible near-infrared (vis-NIR) spectroscopy as a rapid and non-destructive alternative for predicting soil properties and SQIs. This study specifically focused on seven soil indicators that contribute to soil fertility, including pH, organic matter (OM), potassium (K), calcium (Ca), magnesium (Mg), available phosphorous (P), and total nitrogen (TN). These properties play key roles in nutrient availability, pH regulation, and soil structure, influencing soil fertility and overall soil health. By utilizing vis-NIR spectroscopy, we were able to accurately predict the soil indicators with good accuracy using the Cubist model (R2 = 0.35-0.93), offering a cost-effective and environmentally friendly alternative to traditional laboratory analyses. Using the seven soil indicators, we looked at three different approaches for calculating and predicting the SQI, including: (1) measured SQI (SQI_m), which is derived from laboratory-measured soil properties; (2) predicted SQI (SQI_p), which is calculated using predicted soil properties from spectral data; and (3) direct prediction of SQI (SQI_dp), The findings demonstrated that SQI_dp exhibited a higher accuracy (R2 = 0.90) in predicting soil quality compared to SQI_p (R2 = 0.23).

Soil data recency: The foundation for harmonizing soil data across time.

Sustainable soil resource management depends on reliable soil information, often derived from 'legacy soil data' or a combination of old and new soil data. However, the task of harmonizing soil data collected at different times remains a largely unexplored in the literature. Addressing this challenge requires incorporating the temporal dimension into mathematical and statistical models for spatio-temporal soil studies. This study aimed to create a comprehensive framework for harmonizing soil data across various time. We assessed the integration of historical and recent soil data, ranging from 4 to 48 years old data, using soil data recency analysis. To achieve this, we introduced an 'age of data' attribute, calculating the time difference between soil survey years and the present (e.g., 2022). We applied three machine learning models - Decision Trees (DT), Random Forest (RF), Gradient Boosting (GBM) - to a dataset containing 6339 sites and 28,149 depth-harmonized layers. The results consistently demonstrated robust performance across models, RF outperforming with an R-squared value of 0.99, RMSE of 1.41, and a concordance of 0.97. Similarly, DT and GBM also showed strong predictive power. Terrain-derived environmental covariates played a more important role than land use and land cover (LULC) change in predicting soil data recency. While LULC change showed soil organic carbon concentration variability across the different depths, it was a less important factor. Anthropogenic factors, such as LULC change and normalized difference vegetation index (NDVI), were not primary determinants of soil data recency. Variations in soil depth had no impact on predicting soil data recency. This study validated that terrain-derived covariates, especially elevation factors, effectively explain the quality of older soil data when predicting current soil attributes using the soil data recency concept. This approach has the potential to enhance real-time estimates, such as carbon budgets, and we emphasize its importance in global earth system models.

Spectral prediction of soil salinity and alkalinity indicators using visible, near-, and mid-infrared spectroscopy.

Drought and the impacts of climate change have led to an escalation in soil salinity and alkalinity across various regions worldwide, including Iran. The Chahardowli Plain in western Iran, in particular, has witnessed a significant intensification of this phenomenon over the past decade. Consequently, modeling of soil attributes that serve as indicators of soil salinity and alkalinity became a priority in this region. To date, only a limited number of studies have been conducted to assess indicators of salinity and alkalinity through spectrometry across diverse spectral ranges. The spectral ranges encompassing mid-infrared (mid-IR), visible, and near-infrared (vis-NIR) spectroscopy were employed to estimate soil properties including sodium adsorption ratio (SAR), exchangeable sodium ratio (ESR), exchangeable sodium percentage (ESP), pH, and electrical conductivity (EC). Five distinct models were employed: Partial Least Squares Regression (PLSR), bootstrapping aggregation PLSR (BgPLSR), Memory-Based Learning (MBL), Random Forest (RF), and Cubist. The calibration and assessment of model performance were carried out using several key metrics including Ratio of Performance to Deviation (RPD) and the coefficient of determination (R2). Analysis of the outcomes indicates that the accuracy and precision of the mid-IR spectra surpassed that of vis-NIR spectra, except for pH, which exhibited a superior RPD compared to other properties. Notably, in the prediction of pH utilizing vis-NIR reflectance spectra, the BgPLSR model exhibited the highest accuracy and precision, boasting an RPD value of 2.56. In the domain of EC prediction, the PLSR model yielded an RPD of 2.64. For SAR, the MBL model achieved an RPD of 2.70, while ESR prediction benefited from the MBL model with an impressive RPD of 4.36. Likewise, the MBL model demonstrated remarkable precision and accuracy in ESP prediction, garnering an RPD of 4.41. The MBL model's efficacy in forecasting with limited datasets was notably pronounced among the models considered. This study underscores the valuable role of spectral predictions in facilitating the work of soil surveyors in gauging salinity and alkalinity indicators. It is recommended that the integration of spectrometry-based salinity and alkalinity predictions be incorporated into forthcoming soil mapping endeavors within semi-arid and arid regions.

An experimental investigation of the erosion process and morphological characteristics of the tile-back type slope with non-uniform slopes based on a 3D reconstruction method.

Tile-back type slopes comprise ephemeral gullies (EGs) and hillslopes; they are a unique and widely distributed micro-landform in the Loess Plateau region of China. Gully erosion from these landforms is a serious issue, but the micro-landform makes the erosion process and its estimation complex. Quantifying soil erosion processes and their distribution characteristics at different positions on tile-back type slopes will provide a clearer picture for ecological restoration to control further soil degradation. This study investigated the erosion process of tile-back type slope with non-uniform slopes using a 3D photo-reconstruction method during eight successive simulated rainfall events. The results showed that EG erosion began with a chain of intermittent headcuts. When the accumulated rainfall reached 76 mm, serious collapses dramatically increased the amount of sediment by 216% after the first rainfall (cumulative rainfall was about 15 mm). We quantified the sediment contribution of EG erosion (46.20%), rill erosion (35.62%), and inter-rill erosion (18.18%) to total soil loss. The erosion area of the steep slope section and extremely steep slope section accounted for 33.26% and 66.74% of the total erosion area, respectively. Moreover, sediment amounts significantly correlated with morphological parameters, particularly the amount of EG erosion and maximum gully depth, with a correlation coefficient of 0.98. Cumulative gully length and erosion area had the greatest effect on rill erosion, with a correlation coefficient of 0.97. These results provide insight into the qualitative and quantitative understanding of EG erosion process on Loess Plateau of China and an important reference for the rational arrangement of EG control measures.

Modeling the spatial variation of calcium carbonate equivalent to depth using machine learning techniques.

Inorganic carbon is the largest source of carbon in terrestrial surface, particularly in arid and semiarid regions, including the Chahardowli Plain in western Iran. Inorganic carbon plays an equal or greater role than organic soil carbon in these areas, although less attention has been paid in quantifying their variability. The objective of this study was to model and map calcium carbonate equivalent (CCE) presenting inorganic carbon in soil using machine learning and digital soil mapping techniques. Chahardowli Plain in foothills of the Zagros Mountains in the southeast of Kurdistan Province in Iran was taken as a case study area. CCE was measured at 0-5, 5-15, 15-30, 30-60, and 60-100 cm depths following GloalSoilMap.net project specifications. A total of 145 samples were collected from 30 soil profiles using the conditional Latin hypercube (cLHS) method of sampling. Relationships between CCE and environmental predictors were modeled using random forest (RF) and decision tree (DT) models. In general, the RF model performed slightly superior than the DT model. The mean value of CCE increased with soil depth, from 3.5% (0-5 cm) to 63.8% (30-60 cm). Remote sensing (RS) variables and terrestrial variables were equally important. The importance of RS variables was higher at the surface than terrestrial variables, and vice versa. The most significant variables were Channel Network Base Level (CNBL) variable and Difference Vegetation Index (DVI) with the same variable importance value (21.1%). In areas affected by river activities, the use of the CNBL and vertical distance to channel networks (VDCN) as variables in digital soil mapping (DSM) could increase the accuracy of soil property prediction maps. The VDCN played a principal role in soil distribution in the study area by affecting the rate of discharge and, thus, erosion and sedimentation. A high percentage of carbonate in parts of the region could exacerbate nutrient deficiencies for most crops and provide information for sustainably managing agricultural activity.

An Innovative Fusion-Based Scenario for Improving Land Crop Mapping Accuracy.

The accuracy of land crop maps obtained from satellite images depends on the type of feature selection algorithm and classifier. Each of these algorithms have different efficiency in different conditions; therefore, developing a suitable strategy for combining the capabilities of different algorithms in preparing a land crop map with higher accuracy can be very useful. The objective of this study was to develop a fusion-based framework for improving land crop mapping accuracy. First, the features were retrieved using the Sentinel 1, Sentinel 2, and Landsat-8 imagery. Then, training data and various feature selection algorithms including recursive feature elimination (RFE), random forest (RF), and Boruta were used for optimal feature selection. Various classifiers, including artificial neural network (ANN), support vector machine (SVM), and RF, were implemented to create maps of land crops relying on optimal features and training data. After that, in order to increase the result accuracy, maps of land crops derived from several scenarios were fused using a fusion-based voting strategy at the level of decision, and new maps of land crops and classification uncertainty maps were prepared. Subsequently, the performance of different scenarios was evaluated and compared. Among the feature selection algorithms, RF accuracy was higher than RFE and Boruta. Moreover, the efficiency of RF was higher than SVM and ANN. The overall accuracy of the voting scenario was higher than all other scenarios. The finding of this research demonstrated that combining the features' capabilities extracted from sensors in different spectral ranges, different feature selection algorithms, and classifiers improved the land crop classification accuracy.

A Novel Paper-Based Reagentless Dual Functional Soil Test to Instantly Detect Phosphate Infield.

Soil tests for plant-available phosphorus (P) are suggested to provide offsite P analysis required to monitor P fertilizer application and reduce P losses to downstream water. However, procedural and cost limitations of current soil phosphate tests have restricted their widespread use and have made them accessible only in laboratories. This study proposes a novel paper-based reagentless electrochemical soil phosphate sensor to extract and detect soil phosphate using an inexpensive and simple approach. In this test, concentrated Mehlich-3 and molybdate ions were impregnated in filter paper, which served as the phosphate extraction and reaction zone, and was followed by electrochemical detection using cyclic voltammetry signals. Soil samples from 22 sampling sites were used to validate this method against inductively coupled plasma optical emission spectroscopy (ICP) soil phosphate tests. Regression and correlation analyses showed a significant relationship between phosphate determinations by ICP and the proposed method, delivering a correlation coefficient, r, of 0.98 and a correlation slope of 1.02. The proposed approach provided a fast, portable, low-cost, accessible, reliable, and single-step test to extract and detect phosphate simultaneously with minimum waste (0.5 mL per sample), which made phosphate characterization possible in the field.

Modeling potential habitats and predicting habitat connectivity for Leucanthemum vulgare Lam. in northwestern rangelands of Iran.

Invasive plants can alter the function and structure of ecosystems resulting in social, economic, and ecological damage. Effective methods to reduce the dominance of invasive plants are needed. The present study was aimed at modeling the invasive species Leucanthemum vulgare Lam. in the rangelands of the Namin region in northwest Iran, as well as predicting the habitat connectivity of this species to detect areas with high habitat connectivity. Modeling of potential habitats was performed using logistic regression (LR) and maximum entropy (MaxEnt); the ensemble map which resulted from these was used to predict habitat connectivity using the electrical circuit method. Topography (elevation, slope, and aspect), climate (precipitation and temperature), and soil (acidity, electrical conductivity, soil texture, calcium, magnesium, sodium, phosphorus, potassium, organic carbon, organic matter, saturation percentage, and total neutralizing value) were used in this study. The presence and absence points of the L. vulgare were recorded using a stratified-random sampling method by means of a global positioning system. Soil samples were collected at a depth of 0 to 30 cm where L. vulgare was present and also where it was absent. According to the results, in LR, the variables of temperature, phosphorus, organic matter, and sand and in the MaxEnt, the variables of sand, total neutralizing value (TNV), and silt were the most influential factors on the distribution of L. vulgare. The appraisal of the MaxEnt performance and the precision of the model prediction were 0.97. The Kappa indices for the predicted map obtained from the LR and MaxEnt models were 0.80 and 0.73, respectively. The models' evaluation indicated that both models were able to predict the distribution of L. vulgare habitats with a high level of accuracy; however, LR was more reliable. According to the LR prediction, 9.91% (10,556.25 ha) of the Namin region was attacked by L. vulgare. Connectivity assessment showed that the current density spread of L. vulgare continued from the northeast of the Namin region toward the southeast. On the other hand, the higher current density spread was demonstrated in the eastern region (rangelands adjacent to Fandoghlu forests), and other rangelands which are more threatened by the invasion of L. vulgare. Identifying sites exposed to invasive species can help implement programs to prevent invasive species from invading areas where management and prevention should be implanted to prevent and/or reduce the spread.

Rotavirus activates a noncanonical ATM-Chk2 branch of DNA damage response during infection to positively regulate viroplasm dynamics.

Surveillance for maintaining genomic pristineness, a protective safeguard of great onco-preventive significance, has been dedicated in eukaryotic cells to a highly conserved and synchronised signalling cascade called DNA damage response (DDR). Not surprisingly, foreign genetic elements like those of viruses are often potential targets of DDR. Viruses have evolved novel ways to subvert this genome vigilance by twisting canonical DDR to a skewed, noncanonical response through selective hijacking of some DDR components while antagonising the others. Though reported for many DNA and a few RNA viruses, potential implications of DDR have not been addressed yet in case of infection with rotavirus (RV), a double-stranded RNA virus. In the present study, we aimed at the modulation of ataxia telangiectasia mutated (ATM)-checkpoint kinase 2 (Chk2) branch of DDR in response to RV infection in vitro. We found activation of the transducer kinase ATM and its downstream effector Chk2 in RV-SA11-infected cells, the activation response being maximal at 6-hr post infection. Moreover, ATM activation was found to be dependent on induction of the upstream sensor Mre11-Rad50-Nbs1 (MRN) complex. Interestingly, RV-SA11-mediated maximal induction of ATM-Chk2 pathway was revealed to be neither preceded by occurrence of nuclear DNA damage nor transduced to formation of damage-induced canonical nuclear foci. Subsequent investigations affirmed sequestration of MRN components as well as ATM-Chk2 proteins away from nucleus into cytosolic RV replication factories (viroplasms). Chemical intervention targeting ATM and Chk2 significantly inhibited fusion and maturation of viroplasms leading to attenuated viral propagation. Cumulatively, the current study describes RV-mediated activation of a noncanonical ATM-Chk2 branch of DDR skewed in favour of facilitated viroplasm fusion and productive viral perpetuation.

Evaluation of Optimized Preprocessing and Modeling Algorithms for Prediction of Soil Properties Using VIS-NIR Spectroscopy.

The absorbance spectra for air-dried and ground soil samples from Ontario, Canada were collected in the visible and near-infrared (VIS-NIR) region from 343 to 2200 nm. The study examined thirteen combination of six preprocessing (1st derivative, 2nd derivative, Savitzky-Golay, Gap, SNV and Detrend) method included in 'prospectr' R package along with four modeling approaches: partial least square regression (PLSR), cubist, random forest (RF), and extreme learning machine (ELM) for prediction of the soil organic matter (SOM). The 1st derivative + gap, 2nd derivative + gap and standard normal variance (SNV) were the best preprocessing algorithms. Thus, only these three preprocessing algorithms along with four modeling approaches were used for prediction of soil pH, electrical conductively (EC), %sand, %silt, %clay, %very coarse sand (VCS), %coarse sand (CS), %medium sand (ms) and %fine sand (fs). The results showed that OM, pH, %sand, %silt and %CS were all predicted with confidence (R2 > 0.60) and the combination of 1st derivative + gap and RF gained the best performance. A detailed comparison of the preprocessing and modeling algorithms for various soil properties in this study demonstrate that for better prediction of soil properties using VIS-NIR spectroscopy requires different preprocessing and modeling algorithms. However, in general RF and 1st derivative + gap can be labeled at the best combination of preprocessing and modelling algorithms.

Comparison of Heating Strategies on Soil Water Measurement Using Actively Heated Fiber Optics on Contrasting Textured Soils.

The actively heated fiber optics (AHFO) technique has the potential to measure soil water at high spatial and temporal resolutions, and thus it can bridge the measurement gap from point to large scales. However, the availability of power might restrict its use, since high power is required to heat long fiber optic cables under field conditions; this can be a challenge for long-term soil water monitoring under field conditions. This study investigated the performance of different heating strategies (power intensity and heating duration) on soil water measurement by the AHFO technique on three different textured soils. Different heating strategies: high power-short pulses (20 Wm-1-3 min), low power-short pulses (10 Wm-1-3 min, 5 Wm-1-3 min, 2.5 Wm-1-3 min) and low power-long pulses (10 Wm-1-5 min, 5 Wm-1-10 min, 2.5 Wm-1-15 min) were tested using laboratory soil columns. The study compared the sensitivity of the thermal response, NTcum to volumetric water content (VWC) and the predictive error of different heating strategies and soils. Results of this study showed that the sensitivity of NTcum increased and the predictive error decreased with increasing power intensity, irrespective of the soil type. Low power-short heat pulses such as 5 Wm-1-3 min and 2.5 Wm-1-3 min produced high predictive errors, RMSE of 5-6% and 6-7%, respectively. However, extending the heating duration was effective in reducing the error for both 10 and 5 Wm-1 power intensities, but not for the 2.5 Wm-1. The improvement was particularly noticeable in 5 Wm-1 -10 min; it reduced the RMSE by 1.5% (sand and clay loam) and 2.73% (sandy loam). Overall, the results of this study suggested that extending the heating duration of 10 and 5 Wm-1 power intensities can improve the sensitivity of the thermal response and predictive accuracy of the estimated soil water content (SWC). The results are particularly important for field applications of the AHFO technique, which can be limited by the availability of high power, which restricts the use of 20 Wm-1. For example, 5 Wm-1-10 min improved the predictive accuracy to 3-4%, which has the potential to be used for validating soil water estimations at satellite footprint scales. However, the effects of diurnal temperature variations should also be considered, particularly when using low power intensity such as 5 Wm-1 in surface soils under field conditions.

In-Situ Estimation of Soil Water Retention Curve in Silt Loam and Loamy Sand Soils at Different Soil Depths.

The soil water retention curve (SWRC) shows the relationship between soil water (θ) and water potential (ψ) and provides fundamental information for quantifying and modeling soil water entry, storage, flow, and groundwater recharge processes. While traditionally it is measured in a laboratory through cumbersome and time-intensive methods, soil sensors measuring in-situ θ and ψ show strong potential to estimate in-situ SWRC. The objective of this study was to estimate in-situ SWRC at different depths under two different soil types by integrating measured θ and ψ using two commercial sensors: time-domain reflectometer (TDR) and dielectric field water potential (e.g., MPS-6) principles. Parametric models were used to quantify θ-ψ relationships at various depths and were compared to laboratory-measured SWRC. The results of the study show that combining TDR and MPS-6 sensors can be used to estimate plant-available water and SWRC, with a mean difference of -0.03 to 0.23 m3m-3 between the modeled data and laboratory data, which could be caused by the sensors' lack of site-specific calibration or possible air entrapment of field soil. However, consistent trends (with magnitude differences) indicated the potential to use these sensors in estimating in-situ and dynamic SWRC at depths and provided a way forward in overcoming resource-intensive laboratory measurements.

Long-term continuous cropping affects ecoenzymatic stoichiometry of microbial nutrient acquisition: a case study from a Chinese Mollisol.

BACKGROUND: Soil- and plant-produced extracellular enzymes drive nutrient cycling in soils and are assumed to regulate supply and demand for carbon (C) and nutrients within the soil. Thus, agriculture management decisions that alter the balance of plant and supplemental nutrients should directly alter extracellular enzyme activities (EEAs), and EEA stoichiometry in predictable ways. We used a 12-year experiment that varyied three major continuous grain crops (wheat, soybean, and maize), each crossed with mineral fertilizer (WCF, SCF and MCF, respectively) or not fertilized (WC, SC and MC, respectively, as controls). In response, we measured the phospholipid fatty acids (PLFAs), EEAs and their stoichiometry to examine the changes to soil microbial nutrient demand under the continuous cropping of crops, which differed with respect to the input of plant litter and fertilizer. RESULTS: Fertilizer generally decreased soil microbial biomass and enzyme activity compared to non-fertilized soil. According to enzyme stoichiometry, microbial nutrient demand was generally C- and phosphorus (P)-limited, but not nitrogen (N)-limited. However, the degree of microbial resource limitation differed among the three crops. The enzymatic C:N ratio was significantly lower by 13.3% and 26.8%, whereas the enzymatic N:P ratio was significantly higher by 9.9% and 42.4%, in MCF than in WCF and SCF, respectively. The abundances of arbuscular mycorrhizal fungi and aerobic PLFAs were significantly higher in MCF than in WCF and SCF. CONCLUSION: These findings are crucial for characterizing enzymatic activities and their stoichiometries that drive microbial metabolism with respect to understanding soil nutrient cycles and environmental conditions and optimizing practices of agricultural management. © 2021 Society of Chemical Industry.

Impacts of land-use changes on the variability of microbiomes in soil profiles.

BACKGROUND: The conversion of arable land to grassland and/or forested land is a common strategy of restoration because the development of plant communities can inhibit the erosion of soil, increase biodiversity and improve associated ecosystem services. The vertical profiles of microbial communities, however, have not been well characterized and their variability after land conversion is not well understood. We assessed the effects of the conversion of arable land (AL) to grassland (GL) and forested land (FL) on bacterial communities as old as 29 years in 0-200-cm profiles of a Chinese Mollisol. RESULTS: The soil in AL has been a stable ecosystem and changes in the assembly of soil microbiomes tended to be larger in the topsoil. The soil properties and microbial biodiversity of arable land were larger following revegetation and reforestation. The conversion caused a more complex coupling among microbes, and negative interactions and average connectivity were stronger in the 0-20-cm layers in GL and in the 20-60-cm layers in FL. The land use dramatically influenced the assembly of the microbial communities more in GL than AL and FL. The bacterial diversity was an important component of soil multinutrient cycling in the profiles and microbial functions were not as affected by changes in land use. CONCLUSION: The spatial variation of the microbiomes provided critical information on below-ground soil ecology and the ability of the soil to provide crucial ecosystem services. © 2021 Society of Chemical Industry.

Emergence of Novel Coronavirus and COVID-19: whether to stay or die out?

The last century has witnessed several assaults from RNA viruses, resulting in millions of death throughout the world. The 21st century appears no longer an exception, with the trend continued with escalated fear of SARS coronavirus in 2002 and further concern of influenza H5N1 in 2003. A novel influenza virus created the first pandemic of the 21st century, the pandemic flu in 2009 preceded with the emergence of another deadly virus, MERS-CoV in 2012. A novel coronavirus "SARS-CoV-2" (and the disease COVID-19) emerged suddenly, causing a rapid outbreak with a moderate case fatality rate. This virus is continuing to cause health care providers grave concern due to the lack of any existing immunity in the human population, indicating their novelty and lack of previous exposure. The big question is whether this novel virus will be establishing itself in an endemic form or will it eventually die out? Endemic viruses during circulation may acquire mutations to infect naïve, as well as individual with pre-existing immunity. Continuous monitoring is strongly advisable, not only to the newly infected individuals, but also to those recovered individuals who were infected by SARS-CoV-2 as re-infection may lead to the selection of escape mutants and subsequent dissemination to the population.

Small alarmones (p)ppGpp regulate virulence associated traits and pathogenesis of Salmonella enterica serovar Typhi.

How Salmonella enterica serovar Typhi (S. Typhi), an important human pathogen, survives the stressful microenvironments inside the gastrointestinal tract and within macrophages remains poorly understood. We report here that S. Typhi has a bonafide stringent response (SR) system, which is mediated by (p)ppGpp and regulates multiple virulence-associated traits and the pathogenicity of the S. Typhi Ty2 strain. In an iron overload mouse model of S. Typhi infection, the (p)ppGpp0 (Ty2ΔRelAΔSpoT) strain showed minimal systemic spread and no mortality, as opposed to 100% death of the mice challenged with the isogenic wild-type strain. Ty2ΔRelAΔSpoT had markedly elongated morphology with incomplete septa formation and demonstrated severely attenuated motility and chemotaxis due to the loss of flagella. Absence of the Vi-polysaccharide capsule rendered the mutant strain highly susceptible to complement-mediated lysis. The phenotypes of Ty2ΔRelAΔSpoT was contributed by transcriptional repression of several genes, including fliC, tviA, and ftsZ, as found by reverse transcriptase quantitative polymerase chain reaction and gene complementation studies. Finally, Ty2ΔRelAΔSpoT had markedly reduced invasion into intestinal epithelial cells and significantly attenuated survival within macrophages. To the best of our knowledge, this was the first study that addressed SR in S. Typhi and showed that (p)ppGpp was essential for optimal pathogenic fitness of the organism.

Driving Factors and Future Prediction of Land Use and Cover Change Based on Satellite Remote Sensing Data by the LCM Model: A Case Study from Gansu Province, China.

Land use and cover change (LUCC) is an important issue affecting the global environment, climate change, and sustainable development. Detecting and predicting LUCC, a dynamic process, and its driving factors will help in formulating effective land use and planning policy suitable for local conditions, thus supporting local socioeconomic development and global environmental protection. In this study, taking Gansu Province as a case study example, we explored the LUCC pattern and its driving mechanism from 1980 to 2018, and predicted land use and cover in 2030 using the integrated LCM (Logistic-Cellular Automata-Markov chain) model and data from satellite remote sensing. The results suggest that the LUCC pattern was more reasonable in the second stage (2005 to 2018) compared with that in the first stage (1980 to 2005). This was because a large area of green lands was protected by ecological engineering in the second stage. From 1980 to 2018, in general, natural factors were the main force influencing changes in land use and cover in Gansu, while the effects of socioeconomic factors were not significant because of the slow development of economy. Landscape indices analysis indicated that predicted land use and cover in 2030 under the ecological protection scenario would be more favorable than under the historical trend scenario. Besides, results from the present study suggested that LUCC in arid and semiarid area could be well detected by the LCM model. This study would hopefully provide theoretical instructions for future land use planning and management, as well as a new methodology reference for LUCC analysis in arid and semiarid regions.