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Summary: Background: Post-acute sequalae of COVID-19 defines a wide range of ongoing symptoms and conditions long after SARS-CoV-2 infection including respiratory diseases. The histopathological changes in the lung and underlying mechanism remain elusive. Methods: We investigated lung histopathological and transcriptional changes in SARS-CoV-2-infected male hamsters at 7, 14, 42, 84 and 120dpi, and compared with A (H1N1)pdm09 infection. Findings: We demonstrated viral residue, inflammatory and fibrotic changes in lung after SARS-CoV-2 but not H1N1 infection. The most prominent histopathological lesion was multifocal alveolar-bronchiolization observed in every SARS-CoV-2 infected hamster (31/31), from 42dpi to 120dpi. Proliferating (Ki67+) CK14+ basal cells accumulated in alveoli adjacent to bronchioles at 7dpi, where they proliferated and differentiated into SCGB1A+ club cell or Tubulin+ ciliated cells forming alveolar-bronchiolization foci. Molecularly, Notch pathway significantly upregulated with intensive Notch3 and Hes1 protein expression in alveolar-bronchiolization foci at 42 and 120dpi, suggesting Notch signaling involving the persistence of alveolar-bronchiolization. This is further demonstrated by spatial transcriptomic analysis. Intriguingly, significant upregulation of some cell-growth promoting pathways and genes such as Tubb4b, Stxbp4, Grb14 and Mlf1 were spatially overlapping with bronchiolization lesion. Interpretation: Incomplete resolution of SARS-CoV-2 infection in lung with viral residue, chronic inflammatory and fibrotic damage and alveolar-bronchiolization impaired respiratory function. Aberrant activation of CK14+ basal cells during tissue regeneration led to persistent alveolar-bronchiolization due to sustained Notch signaling. This study advances our understanding of respiratory PASC, sheds light on disease management and highlights the necessity for monitoring disease progression in people with respiratory PASC. Funding: Funding is listed in the Acknowledgements section.

Stover mulching, as a sustainable agricultural conservation practice, has been shown to effectively increase soil organic matter and enhance crop yields. The impact of stover mulching on soil microorganisms has been extensively studied. However, less attention has been given to endophytic and rhizospheric microorganisms that have closer relationships with crops. How do the quality and frequency of stover mulching affect the composition and structure of these endosphere and rhizosphere microbial communities? And what is their influence on critical indicators of soil health such as bacterial plant pathogen and Rhizobiales? These questions remain unresolved. Therefore, we investigated the responses of the microbial functional guilds in the endosphere and rhizosphere to maize stover mulching qualities (0%, 33%, 67%, and total stover mulching every year) and frequencies (once every 3 years and twice every 3 years) under 10-year no-till management. Results showed significant correlations between Bacillales and Rhizobiales orders and soil SOC, NO3−N, and NH4+N; Hypocreales and Eurotiales orders were significantly correlated with soil NO3−N, with the Aspergillus genus also showing a significant correlation with soil SOC. The frequency and quality of stover mulching had a significant effect on root and rhizospheric microbial communities, with the lowest relative abundance of bacterial plant pathogens and highest relative abundance of nitrogen-fixing bacteria such as Rhizobiales and Hypocreales observed under F1/3 and F2/3 conditions. The most complex structures in endosphere and rhizospheric microbial communities were found under Q33 and Q67 conditions, respectively. This research indicates that from a soil health perspective, low-frequency high-coverage stover mulching is beneficial for the composition of endosphere and rhizosphere microbial communities, while moderate coverage levels are conducive to more complex structures within these communities. This study holds significant ecological implications for agricultural production and crop protection.

Children infected by SARS-CoV-2 Omicron variant may develop neurological complications. To study the pathogenesis in the growing brain, we intranasally challenged newly-weaned or mature hamsters with SARS-CoV-2 Omicron BA.2, BA.5, or Delta variant. Omicron BA.2 and Delta infection produced a significantly lower viral load in the lung tissues of newly-weaned than mature hamsters despite comparable histopathological damages. Newly-weaned hamsters had higher brain viral load, significantly increased cerebrospinal fluid concentration of TNF-α and CXCL10 and inflammatory damages including mild meningitis and parenchymal vascular congestion, despite sparse expression of nucleocapsid antigen in brain cells. Furthermore, 63.6% (28/44) of all SARS-CoV-2 infected newly-weaned hamsters showed microgliosis in olfactory bulb (OB), cerebral cortex, and hippocampus. In infected mature hamsters, microgliosis was observed mainly in OB and olfactory cortex of 35.3% (12/34) of their brains. Neuronal degeneration was found in 75% (33/44) of newly-weaned hamsters affecting multiple regions including OB, olfactory cortex, midbrain cortex, and hippocampus, while such changes were mainly observed in the hippocampus of mature hamsters. Importantly, similar brain histopathology was also observed in Omicron BA.5-infected newly-weaned hamsters. Our study suggested that SARS-CoV-2 may affect the brain at a young age. This kind of brain involvement and histological changes are not virus variant or subvariant specific. Incidentally, a moderate amount of eosinophilic infiltration was observed in the mucosa of nasal turbinate and trachea of newly-weaned hamsters infected by Omicron BA.2 and BA.5 but not Delta variant. This histological finding is consistent with the higher incidence of laryngotracheobronchitis in young children infected by the Omicron variant.Summary Intranasal infection of newly-weaned Syrian hamsters by SARS-CoV-2 Omicron variants can lead to brain inflammation and neuron degeneration with detectable low level of viral load and sparse expression of viral nucleoprotein.

IntroductionOwing to challenges in the study of complex rhizosphere and endophytic microbial communities, the composition and function of such microbial communities in steppe ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere and endophytic microbes of the dominant plant species across the Inner Mongolian steppes using metagenomic sequencing and investigated their relationships with changes in mean annual temperature (MAT) and mean annual precipitation (MAP).MethodsMetagenomic sequencing based on Illumina high-throughput sequencing, using the paired end method to construct a small fragment library for sequencing.ResultsAdaptation of root systems to the environment affected the composition and function of rhizosphere and endophytic microbial communities. However, these communities exhibited distinct community assembly and environmental adaptation patterns. Both rhizosphere and endophytic microbial communities can be divided into two unrelated systems based on their ecological niches. The composition and function of the rhizosphere microbial communities were mainly influenced by MAT, while those of the endophytic microbial communities were mainly influenced by MAP. MAT affected the growth, reproduction, and lipid decomposition of rhizosphere microorganisms, whereas MAP affected reverse transcription and cell wall/membrane/envelope biogenic functions of endophytic microorganisms.ConclusionOur findings reveal the composition and function of the rhizosphere and endophytic microbial communities in response to changes in MAP and MAT, which has important implications for future biogeography and climate change research.

Older individuals are at higher risk of SARS-CoV-2 infection and severe outcomes, but the underlying mechanisms are incompletely understood. In addition, how age modulates SARS-CoV-2 re-infection and vaccine breakthrough infections remain largely unexplored. Here, we investigated age-associated SARS-CoV-2 pathogenesis, immune responses, and the occurrence of re-infection and vaccine breakthrough infection utilizing a wild-type C57BL/6N mouse model. We demonstrated that interferon and adaptive antibody response upon SARS-CoV-2 challenge are significantly impaired in aged mice compared to young mice, which results in more effective virus replications and severe disease manifestations in the respiratory tract. Aged mice also showed increased susceptibility to re-infection due to insufficient immune protection acquired during the primary infection. Importantly, two-dose COVID-19 mRNA vaccination conferred limited adaptive immune response among the aged mice, making them susceptible to SARS-CoV-2 infection. Collectively, our findings call for tailored and optimized treatments and prevention strategies against SARS-CoV-2 among older individuals.

Summary: Phages widely exist in numerous environments from wastewater to deep ocean, representing a huge virus diversity, yet remain poorly characterized. Among them, jumbo phages are of particular interests due to their large genome (>200 kb) and unusual biology. To date, only six strains of jumbo phages infecting Klebsiella pneumoniae have been described. Here, we report the isolation and characterization of two jumbo phages from hospital wastewater representing the sixth genus: φKp5130 and φKp9438. Both phages showed lytic activity against broad range of clinical antibiotic-resistant K. pneumoniae strains and distinct physiology including long latent period, small burst size, and high resistance to thermal and pH stress. The treatment of sewage water with the phages cocktail resulted in dramatic decline in K. pneumoniae population. Overall, this study provides detailed molecular and genomics characterization of two novel jumbo phages, expands viral diversity, and provides novel candidate phages to facilitate environmental wastewater treatment.

Studies investigating the diversity and structure of soil microbial systems in response to ionizing radiation are scarce. In particular, effects of long-term low-dose radiation is rarely studied because of its unique conditions. In this study, an area in Chengdu, China, which has been irradiated by the radionuclide thorium-232 for more than 10 years was investigated. Four groups of samples with absorbed dose rates ranging from 192.906 ± 5.05 to 910.964 ± 41.09 nGy/h were collected to analyze the compositional and functional changes of the soil microbial systems in the region. The diversity and structure of the soil microbial systems were determined using high-throughput sequencing. Our results showed that long-term low-dose ionizing radiation had no significant effect on soil bacterial diversity, but had a great impact on fungal diversity. Long-term ionizing radiation strongly affected soil microbial community structure. Long-term low-dose ionizing radiation was shown to have a promoting effect on iron-oxidizing bacteria and ectomycorrhizal fungi and have an inhibiting effect on predatory or parasitic fungi, further affecting the soil C/N ratio. This study is of great reference significance for future research on the impact of long-term low-dose ionizing radiation on soil ecosystems.

Summary: Background: Obesity is a worldwide epidemic and is considered a risk factor of severe manifestation of Coronavirus Disease 2019 (COVID-19). The pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and host responses to infection, re-infection, and vaccination in individuals with obesity remain incompletely understood. Methods: Using the diet-induced obese (DIO) mouse model, we studied SARS-CoV-2 Alpha- and Omicron BA.1-induced disease manifestations and host immune responses to infection, re-infection, and COVID-19 mRNA vaccination. Findings: Unlike in lean mice, Omicron BA.1 and Alpha replicated to comparable levels in the lungs of DIO mice and resulted in similar degree of tissue damages. Importantly, both T cell and B cell mediated adaptive immune responses to SARS-CoV-2 infection or COVID-19 mRNA vaccination are impaired in DIO mice, leading to higher propensity of re-infection and lower vaccine efficacy. However, despite the absence of neutralizing antibody, vaccinated DIO mice are protected from lung damage upon Omicron challenge, accompanied with significantly more IFN-α and IFN-β production in the lung tissue. Lung RNAseq and subsequent experiments indicated that COVID-19 mRNA vaccination in DIO mice boosted antiviral innate immune response, including the expression of IFN-α, when compared to the nonvaccinated controls. Interpretation: Our findings suggested that COVID-19 mRNA vaccination enhances host innate antiviral responses in obesity which protect the DIO mice to a certain degree when adaptive immunity is suboptimal. Funding: A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.

The current study proposes a novel method of preparing Ti–Al–V alloy by electrochemical co-deposition by adding Ti2O3 and V2O3 into the molten salt system. The influence of chlorination of Ti2O3 and V2O3 in KCl–LiCl–MgCl2–AlCl3 melt was studied by inductively-coupled plasma emission spectrometer (ICP-AES) and X-ray diffractometer (XRD). The results revealed that the optimal chlorination temperature ranged from 600 °C to 700 °C and the main chlorination products were TiCl3, VCl3, and Al2O3 byproduct. The electrochemical behavior of Ti3+, V3+ and Al3+ in a molten AlCl3-containing chloride salt was investigated by cyclic voltammetry. The stepwise reduction in the cathode could be given as: V3+→V2+, Ti3+→Ti2+, V2+→V, Ti2+→Ti, Ti2+/V2+/Al3+→Ti–Al–V alloy. The electrolytic products were also characterized by XRD and scanning electron microscopy (SEM), equipped with energy dispersive spectroscopy (EDS). The results demonstrated that, as metallic Al was used as an anode, a dendritic Al3Ti alloy and Al sheet were obtained after the addition of Ti2O3 into the KCl–LiCl–MgCl2–AlCl3 melt. However, the presence of both Ti2O3 and V2O3 resulted in fishbone-like Al3Ti, Al3Ti0.8V0.2 and Al3Ti0.666V0.333 alloys, as well as dense granules of metallic Al.

Stover mulching as a conservation and sustainable agricultural practice is beneficial for maintaining soil nitrogen (N) requirements and plant health. The microbial functional guilds of the root and rhizosphere are important factors in the soil nitrogen cycle. However, it is unclear how the frequency and amount of stover mulching influence microbial functional guilds in the root and rhizosphere. Therefore, we investigated the responses of the microbial functional guilds in the endosphere and rhizosphere to maize stover mulching amounts (0, 1/3, 2/3, and total stover mulching every year) and frequencies (once every 3 years and twice every 3 years) under 10-year no-till management. The bacterial functional guilds of nitrogen fixation, nitrification, and anaerobic nitrate oxidation displayed the significantly correlation with C/N, total nitrogen, NO3−, and NH4+. The fungal functional guilds of plant pathogens and saprotrophs showed significantly correlations with C/N, total nitrogen, and NO3−. Moreover, we found that bacterial guilds play a pivotal role in maintaining N requirements at the jointing stage, whereas root endophytic fungal guilds play a more important role than bacterial guilds in regulating plant health at the mature stage. The frequency and amount of stover mulching had significant effects on the microbial functional guilds in the root and rhizosphere. Our data suggest that stover mulch application twice every 3 years is the optimal mulching frequency because it yielded the lowest abundance of nitrifying and anaerobic nitrate-oxidising bacteria and the highest abundance of nitrogen-fixing bacteria at the jointing stage, as well as the lowest abundance of fungal plant pathogens in roots at the mature stage.

Abstract We conducted a field investigation and evaluation of 13C natural abundance to determine the growth habit and propagation strategy of Acer catalpifolium Rehd., a tree species native to China that is highly endangered. The results showed that A. catalpifolium is a K‐selected strategist and pioneer species. Its narrow ecological range limits its geographical distribution, and poor fecundity limits its population size. The analysis of 13C natural abundance showed that A. catalpifolium does not use organic matter for reproduction when its stand volume is less than 1.08 × 106 cm3 or it is less than 18.6 m tall, but it does use this strategy when it has a sufficient 1.08 × 106 cm3 stand volume or more or is taller than 18.6 m. If environmental conditions are not conducive (e.g., severe human disturbance, cliff edges, or fierce interspecific competition) to the continued growth of the tree, A. catalpifolium may allocate organic matter for reproduction. Human disturbance seems to promote the population expansion of A. catalpifolium. We provide our suggestions for the promotion and protection of A. catalpifolium as a species.

Abstract Background COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genomes reported. One reason is that the challenges underneath sequencing SARS-CoV-2 directly from clinical samples have not been completely tackled, i.e., sequencing samples with low viral load often results in insufficient viral reads for analyses. Methods We applied a novel multiplex PCR amplicon (amplicon)-based and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of SARS-CoV-2 from serials dilutions of a cultured isolate, and eight clinical samples covering a range of sample types and viral loads. We also examined and compared the sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. Results We demonstrated that both amplicon and capture methods efficiently enriched SARS-CoV-2 content from clinical samples, while the enrichment efficiency of amplicon outran that of capture in more challenging samples. We found that capture was not as accurate as meta and amplicon in identifying between-sample variations, whereas amplicon method was not as accurate as the other two in investigating within-sample variations, suggesting amplicon sequencing was not suitable for studying virus-host interactions and viral transmission that heavily rely on intra-host dynamics. We illustrated that meta uncovered rich genetic information in the clinical samples besides SARS-CoV-2, providing references for clinical diagnostics and therapeutics. Taken all factors above and cost-effectiveness into consideration, we proposed guidance for how to choose sequencing strategy for SARS-CoV-2 under different situations. Conclusions This is, to the best of our knowledge, the first work systematically investigating inter- and intra-individual variations of SARS-CoV-2 using amplicon- and capture-based whole-genome sequencing, as well as the first comparative study among multiple approaches. Our work offers practical solutions for genome sequencing and analyses of SARS-CoV-2 and other emerging viruses.

Plant leaf functional traits can reflect the adaptive strategies of plants to environmental changes. Exploring the patterns and causes of geographic variation in leaf functional traits is pivotal for improving ecological theory at the macroscopic scale. In order to explore the geographical variation and the dominant factors of leaf functional traits in the forest ecosystems of China, we measured 15 environmental factors on 16 leaf functional traits in 33 forest reserves in China. The results showed leaf area (LA), carbon-to-nitrogen ratio (C/N), carbon-to-phosphorus ratio (C/P), nitrogen-to-phosphorus ratio (N/P), phosphorus mass per area (Pa) and nitrogen isotope abundance (δ15N)) were correlated with latitude significantly. LA, Pa and δ15N were also correlated with longitude significantly. The leaf functional traits in southern China were predominantly affected by climatic factors, whereas those in northern China were mainly influenced by soil factors. Mean annual temperature (MAT), mean annual precipitation (MAP) and mean annual humidity (MAH) were shown to be the important climate factors, whereas available calcium (ACa), available potassium (AK), and available magnesium (AMg) were shown to be the important climate factors that affect the leaf functional traits of the forests in China. Our study fills the gap in the study of drivers and large-scale geographical variability of leaf functional traits, and our results elucidate the operational mechanisms of forest–soil–climate systems. We provide reliable support for modeling global forest dynamics.

Root-exudate inputs can stimulate the decomposition of soil organic carbon by priming microbial activity, but its ecological significance is still not fully understood. This study evaluated autotrophic respiration and heterotrophic respiration driven by roots using the 13C natural abundance method in a Robinia pseudoacacia plantation. The results showed that the priming effect existed in deep soil of the plantation. The proportions of autotrophic respiration and heterotrophic respiration deriving from priming effect to total soil respiration varied with soil depth. Rhizomicrobial respiration (RMR) accounted for about 15% of the total soil respiration, and the rate of priming decomposition of soil organic matter (PSOM) was only about 5% of the total soil respiration. RMR was significantly positively correlated with PSOM. Heterotrophic respiration derived by the priming effect was too weak to have a positive impact on atmospheric CO2.

Rhizosphere microbes in forests are key elements of the carbon sequestration of terrestrial ecosystems. To date, little is known about how the diversity and species interactions of the active rhizomicrobial community change during soil carbon sequestration and what interactions drive these changes. In this study, we used a combination of DNA and stable isotope method to explore correlations between the composition of microbial communities, N transformation, and the sequestration de novo of carbon in soils around Pinus tabuliformis and Quercus variabilis roots in North China. Rhizosphere soils from degraded lands, primary stage land (tree roots had colonized in degraded soil for 1 year), and nature forest were sampled for analyses. The results showed that microbial communities and newly sequestered soil organic carbon (SOC) contents changed with different tree species, environments, and successive stages. The fungal unweighted and weighted UniFrac distances could better show the different microbial species structures and differences in successive stages. Newly sequestered SOC was positively correlated with the bacterial order Rhizobiales (in P. tabuliformis forests), the fungal order Russulales (in Q. variabilis forests), and δ15N. Consequently, the bacterial order Rhizobiales acted as an important taxa for P. tabuliformis root-driven carbon sequestration, and the fungal order Russulales acted as an important taxa for Q. variabilis root-driven carbon sequestration. The two plant species allocated root exudates to different portion of their root systems, which in turn altered microbial community composition and function. The δ15N of soil organic matter could be an important indicator to estimate root-driven carbon sequestration.

In biology, it is often critical to determine the identity of an organism and phenotypic traits of interest. Whole-genome sequencing can be useful for this but has limited power for trait prediction. However, we can take advantage of the inherent information content of phenotypes to bypass these limitations. We demonstrate, in clinical and environmental bacterial isolates, that growth dynamics in standardized conditions can differentiate between genotypes, even among strains from the same species. We find that for pairs of isolates, there is little correlation between genetic distance, according to phylogenetic analysis, and phenotypic distance, as determined by growth dynamics. This absence of correlation underscores the challenge in using genomics to infer phenotypes and vice versa. Bypassing this complexity, we show that growth dynamics alone can robustly predict antibiotic responses. These findings are a foundation for a method to identify traits not easily traced to a genetic mechanism. [ABSTRACT FROM AUTHOR]

We conducted a field investigation and evaluation of 13C natural abundance to determine the growth habit and propagation strategy of Acer catalpifolium Rehd., a tree species native to China that is highly endangered. The results showed that A. catalpifolium is a K-selected strategist and pioneer species. Its narrow ecological range limits its geographical distribution, and poor fecundity limits its population size. The analysis of 13C natural abundance showed that A. catalpifolium does not use organic matter for reproduction when its stand volume is less than 1.08 x 106 cm³ or it is less than 18.6 m tall, but it does use this strategy when it has a sufficient 1.08 x 106 cm³ stand volume or more or is taller than 18.6 m. If environmental conditions are not conducive (e.g., severe human disturbance, cliff edges, or fierce interspecific competition) to the continued growth of the tree, A. catalpifolium may allocate organic matter for reproduction. Human disturbance seems to promote the population expansion of A. catalpifolium. We provide our suggestions for the promotion and protection of A. catalpifolium as a species. [ABSTRACT FROM AUTHOR]

sensitive and effective method for simultaneous determination of triazolopyrimidine sulfonamide herbicide residues in soil, water, and wheat was developed using ultra-performance liquid chromatography coupled with tandem mass spectrometry. The four herbicides (pyroxsulam, flumetsulam, metosulam, and diclosulam) were cleaned up with an off-line C18 SPE cartridge and detected by tandem mass spectrometry using an electrospray ionization source in positive mode (ESI+). The determination of the target compounds was achieved in <2.0 min. The limits of detection were below 1 μg kg, while the limits of quantification did not exceed 3 μg kg in different matrices. Quantitation was determined from calibration curves of standards containing 0.05-100 μg L with r > 0.997. Recovery studies were conducted at three spiked levels (0.2, 1, and 5 μg kg for water; 5, 10, and 100 μg kg for soil and wheat). The overall average recoveries for this method in water, soil, wheat plants, and seeds at three levels ranged from 75.4% to 106.0%, with relative standard deviations in the range of 2.1-12.5% ( n = 5) for all analytes. [ABSTRACT FROM AUTHOR]

Enterotoxigenic Escherichia coli (ETEC) is a diverse and poorly characterized E. coli pathotype that causes diarrhea in humans and animals. Phages have been proposed for the veterinary biocontrol of ETEC, but effective solutions require understanding of porcine ETEC diversity that affects phage infection. Here, we sequenced and analyzed the genomes of the PHAGEBio ETEC collection, gathering 79 diverse ETEC strains isolated from European pigs with post-weaning diarrhea (PWD). We ident ified the virulence factors characterizing the pathotype and several antibiotic resistance genes on plasmids, while phage resistance genes and other virulence factors were mostly chromosome encoded. We experienced that ETEC strains were highly resistant to Enterobacteriaceae phage infection. It was only by enrichment of numerous diverse samples with different media and conditions, using the 41 ETEC strains of our collection as hosts, that we could isolate two lytic phages that could infect a large part of our diverse ETEC collection: vB_EcoP_ETEP21B and vB_EcoS_ETEP102. Based on genome and host range analyses, we discussed the infection strategies of the two phages and identified components of lipopolysaccharides (LPS) as receptors for the two phages. Our detailed computational structural analysis highlights several loops and pockets in the tail fibers that may allow recognition and binding of ETEC strains, also in the presence of O-antigens. Despite the importance of receptor recognition, the diversity of the ETEC strains remains a significant challenge for isolating ETEC phages and developing sustainable phage-based products to address ETEC-induced PWD. [ABSTRACT FROM AUTHOR]