Warming and altered precipitation independently and interactively suppress alpine soil microbial growth in a decadal-long experiment

Warming and precipitation anomalies affect terrestrial carbon balance partly through altering microbial eco-physiological processes (e.g., growth and death) in soil. However, little is known about how such processes responds to simultaneous regime shifts in temperature and precipitation. We used the 18O-water quantitative stable isotope probing approach to estimate bacterial growth in alpine meadow soils of the Tibetan Plateau after a decade of warming and altered precipitation manipulation. Our results showed that the growth of major taxa was suppressed by the single and combined effects of temperature and precipitation, eliciting 40-90% of growth reduction of whole community. The antagonistic interactions of warming and altered precipitation on population growth were common (~70% taxa), represented by the weak antagonistic interactions of warming and drought, and the neutralizing effects of warming and wet. The members in Solirubrobacter and Pseudonocardia genera had high growth rates under changed climate regimes. These results are important to understand and predict the soil microbial dynamics in alpine meadow ecosystems suffering from multiple climate change factors.

Carbon starvation raises capacities in bacterial antibiotic resistance and viral auxiliary carbon metabolism in soils

Organic carbon availability in soil is crucial for shaping microbial communities, yet, uncertainties persist concerning microbial adaptations to carbon levels and the ensuing ecological and evolutionary consequences. We investigated organic carbon metabolism, antibiotic resistance, and virus-host interactions in soils subjected to 40 y of chemical and organic fertilization that led to contrasting carbon availability: carbon-poor and carbon-rich soils, respectively. Carbon-poor soils drove the enrichment of putative genes involved in organic matter decomposition and exhibited specialization in utilizing complex organic compounds, reflecting scramble competition. This specialization confers a competitive advantage of microbial communities in carbon-poor soils but reduces their buffering capacity in terms of organic carbon metabolisms, making them more vulnerable to environmental fluctuations. Additionally, in carbon-poor soils, viral auxiliary metabolic genes linked to organic carbon metabolism increased host competitiveness and environmental adaptability through a strategy akin to "piggyback the winner." Furthermore, putative antibiotic resistance genes, particularly in low-abundance drug categories, were enriched in carbon-poor soils as an evolutionary consequence of chemical warfare (i.e., interference competition). This raises concerns about the potential dissemination of antibiotic resistance from conventional agriculture that relies on chemical-only fertilization. Consequently, carbon starvation resulting from long-term chemical-only fertilization increases microbial adaptations to competition, underscoring the importance of implementing sustainable agricultural practices to mitigate the emergence and spread of antimicrobial resistance and to increase soil carbon storage.

Stat3 activation-triggered transcriptional networks govern the early stage of HBV-induced hepatic inflammation

The chronic carrier state of the hepatitis B virus (HBV) often leads to the development of liver inflammation as carriers age. However, the exact mechanisms that trigger this hepatic inflammation remain poorly defined. We analyzed the sequential processes during the onset of liver inflammation based on time-course transcriptome and transcriptional regulatory networks in an HBV transgenic (HBV-Tg) mice model and chronic HBV-infected (CHB) patients (data from GSE83148). The key transcriptional factor (TF) responsible for hepatic inflammation occurrence was identified and then validated both in HBV-Tg mice and liver specimens from young CHB patients. By time-course analysis, an early stage of hepatic inflammation was demonstrated in 3-month-old HBV-Tg mice: a marked upregulation of genes related to inflammation (Saa1/2, S100a8/9/11, or Il1β), innate immunity (Tlr2, Tlr7, or Tlr8), and cells chemotaxis (Ccr2, Cxcl1, Cxcl13, or Cxcl14). Within CHB samples, a unique early stage of inflammation activation was discriminated from immune tolerance and immune activation groups based on distinct gene expression patterns. Enhanced activation of TF Stat3 was strongly associated with increased inflammatory gene expression in this early stage of inflammation. Expression of phosphorylated Stat3 was higher in liver specimens from young CHB patients with relatively higher alanine aminotransferase levels. Specific inhibition of Stat3 activation significantly attenuated the degree of liver inflammation, the expression of inflammation-related genes, and the inflammatory monocytes and macrophages in 3-month-old HBV-Tg mice. Stat3 activation is essential for hepatic inflammation occurrence and is a novel indicator of early-stage immune activation in chronic HBV carriers.

IMPORTANCE

Until now, it remains a mystery that chronic hepatitis B virus (HBV)-infected patients in the "immune tolerance phase" will transition to the "immune activation phase" as they age. In this study, we reveal that Stat3 activation-triggered hepatic transcriptional alterations are distinctive characteristics of the early stage of immune/inflammation activation in chronic HBV infection. For the first time, we discover a mechanism that might trigger the transition from immune tolerance to immune activation in chronic HBV carriers.

Microbial phosphorus-cycling genes in soil under global change

The ongoing climate change on the Tibetan Plateau, leading to warming and precipitation anomalies, modifies phosphorus (P) cycling in alpine meadow soils. However, the interactions and cascading effects of warming and precipitation changes on the key "extracellular" and "intracellular" P cycling genes (PCGs) of bacteria are largely unknown for these P-limited ecosystems. We used metagenomics to analyze the individual and combined effects of warming and altered precipitation on soil PCGs and P transformation in a manipulation experiment. Warming and increased precipitation raised Olsen-P (bioavailable P, AP) by 13% and 20%, respectively, mainly caused by augmented hydrolysis of organic P compounds (NaOH-Po). The decreased precipitation reduced soil AP by 5.3%. The richness and abundance of the PCGs' community in soils on the cold Tibetan plateau were more sensitive to warming than altered precipitation. The abundance of PCGs and P cycling processes decreased under the influence of individual climate change factors (i.e., warming and altered precipitation alone), except for the warming combined with increased precipitation. Pyruvate metabolism, phosphotransferase system, oxidative phosphorylation, and purine metabolism (all "intracellular" PCG) were closely correlated with P pools under climate change conditions. Specifically, warming recruited bacteria with the phoD and phoX genes, which encode enzymes responsible for phosphoester hydrolysis (extracellular P cycling), strongly accelerated organic P mineralization and so, directly impacted P bioavailability in alpine soil. The interactions between warming and altered precipitation profoundly influenced the PCGs' community and facilitated microbial adaptation to these environmental changes. Warming combined with increased precipitation compensated for the detrimental impacts of the individual climate change factors on PCGs. In conclusion, warming combined with rising precipitation has boosting effect on most P-related functions, leading to the acceleration of P cycling within microbial cells and extracellularly, including mineralization and more available P release for microorganisms and plants in alpine soils.

Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate

Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.

Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice

The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.

IMPORTANCE

The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.

Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils

Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.

Nanocurvature-induced field effects enable control over the activity of single-atom electrocatalysts

Tuning interfacial electric fields provides a powerful means to control electrocatalyst activity. Importantly, electric fields can modify adsorbate binding energies based on their polarizability and dipole moment, and hence operate independently of scaling relations that fundamentally limit performance. However, implementation of such a strategy remains challenging because typical methods modify the electric field non-uniformly and affects only a minority of active sites. Here we discover that uniformly tunable electric field modulation can be achieved using a model system of single-atom catalysts (SACs). These consist of M-N4 active sites hosted on a series of spherical carbon supports with varying degrees of nanocurvature. Using in-situ Raman spectroscopy with a Stark shift reporter, we demonstrate that a larger nanocurvature induces a stronger electric field. We show that this strategy is effective over a broad range of SAC systems and electrocatalytic reactions. For instance, Ni SACs with optimized nanocurvature achieved a high CO partial current density of ~400 mA cm-2 at >99% Faradaic efficiency for CO2 reduction in acidic media.

Acidic media enables oxygen-tolerant electrosynthesis of multicarbon products from simulated flue gas

Renewable electricity powered electrochemical CO2 reduction (CO2R) offers a valuable method to close the carbon cycle and reduce our overreliance on fossil fuels. However, high purity CO2 is usually required as feedstock, which potentially decreases the feasibility and economic viability of the process. Direct conversion of flue gas is an attractive option but is challenging due to the low CO2 concentration and the presence of O2 impurities. As a result, up to 99% of the applied current can be lost towards the undesired oxygen reduction reaction (ORR). Here, we show that acidic electrolyte can significantly suppress ORR on Cu, enabling generation of multicarbon products from simulated flue gas. Using a composite Cu and carbon supported single-atom Ni tandem electrocatalyst, we achieved a multicarbon Faradaic efficiency of 46.5% at 200 mA cm-2, which is ~20 times higher than bare Cu under alkaline conditions. We also demonstrate stable performance for 24 h with a multicarbon product full-cell energy efficiency of 14.6%. Strikingly, this result is comparable to previously reported acidic CO2R systems using pure CO2. Our findings demonstrate a potential pathway towards designing efficient electrolyzers for direct conversion of flue gas to value-added chemicals and fuels.

Multiomics Reveals Mechanisms of Alternaria oxytropis Inhibiting Pathogenic Fungi in Oxytropis ochrocephala

Endophytic fungi can benefit the host plant and increase the plant resistance. Now, there is no in-depth study of how Alternaria oxytropis (A. oxytropis) is enhancing the ability of inhibiting pathogenic fungi in Oxytropis ochrocephala (O. ochrocephala). In this study, the fungal community and metabolites associated with endophyte-infected (EI) and endophyte-free (EF) O. ochrocephala were compared by multiomics. The fungal community indicated that there was more A. oxytropis, less phylum Ascomycota, and less genera Leptosphaeria, Colletotrichum, and Comoclathris in the EI group. As metabolic biomarkers, the levels of swainsonine and apigenin-7-O-glucoside-4-O-rutinoside were significantly increased in the EI group. Through in vitro validation experiments, swainsonine and apigenin-7-O-glucoside-4-O-rutinoside can dramatically suppress the growth of pathogenic fungi Leptosphaeria sclerotioides and Colletotrichum americae-borealis by increasing the level of oxidative stress. This work suggested that O. ochrocephala containing A. oxytropis could increase the resistance to fungal diseases by markedly enhancing the content of metabolites inhibiting pathogenic fungi.

Nutrient status changes bacterial interactions in a synthetic community

Microbial interactions affect community stability and niche spaces in all ecosystems. However, it is not clear what factors influence these interactions, leading to changes in species fitness and ecological niches. Here, we utilized 16 monocultures and their corresponding pairwise co-cultures to measure niche changes among 16 cultivable bacterial species in a wide range of carbon sources, and we used resource availability as a parameter to alter the interactions of the synthetic bacterial community. Our results suggest that metabolic similarity drives niche deformation between bacterial species. We further found that resource limitation resulted in increased microbial inhibition and more negative interactions. At high resource availability, bacteria exhibited little inhibitory potential and stronger facilitation (in 71% of cases), promoting niche expansion. Overall, our results show that metabolic similarity induces different degrees of resource competition, altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. This framework may lay the basis for understanding complex niche deformation and microbial interactions as modulated by metabolic similarity and resource availability.IMPORTANCEUnderstanding the intricate dynamics of microbial interactions is crucial for unraveling the stability and ecological roles of diverse ecosystems. However, the factors driving these interactions, leading to shifts in species fitness and ecological niches, remain inadequately explored. We demonstrate that metabolic similarity serves as a key driver of niche deformation between bacterial species. Resource availability emerges as a pivotal parameter, affecting interactions within the community. Our findings reveal heightened microbial inhibition and more negative interactions under resource-limited conditions. The prevalent facilitation is observed under conditions of high resource availability, underscoring the potential for niche expansion in such contexts. These findings emphasize that metabolic similarity induces varying degrees of resource competition, thereby altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. Our workflow has broad implications for understanding the roles of metabolic similarity and resource availability in microbial interactions and for designing synthetic microbial communities.

Use of metagenomic next-generation sequencing for diagnosis of peritonitis in end-stage liver disease

Background: Conventional methods are low in positive rates and time-consuming for ascites pathogen detection in patients with end-stage liver disease (ESLD). With many advantages, metagenomic next-generation sequencing (mNGS) may be a good alternative method. However, the related studies are still lacking. Methods: Ascites from 50 ESLD patients were sampled for pathogen detection using mNGS and conventional methods (culture and polymorphonuclear neutrophils detection) in this prospective observational study. Results: Forty-two samples were detected positive using mNGS. 29 strains of bacteria, 11 strains of fungi, and 9 strains of viruses were detected. 46% of patients were detected to be co-infected with 2 or more pathogens by mNGS. Moreover, mNGS showed similar and high positive rates in ESLD patients with different clinical characteristics. Compared to conventional methods, mNGS had higher positivity rates (84% vs. 20%, P<0.001), sensitivity (45.2% vs. 23.8%, P=0.039), broader pathogen spectrum, shorter detection time (24 hours vs. 3-7 days), but lower specificity (25% vs 100%, P = 0.010). Furthermore, compared to conventional methods, mNGS showed similar consistence with final diagnosis (42% vs. 36%, P=0.539). Conclusions: mNGS may be a good supplement for conventional methods and helpful to early etiological diagnosis of peritonitis, and thus improve ESLD patients' survival.

Elevational distribution and seasonal dynamics of alpine soil prokaryotic communities

The alpine grassland ecosystem is a biodiversity hotspot of plants on the Qinghai-Tibetan Plateau, where rapid climate change is altering the patterns of plant biodiversity along elevational and seasonal gradients of environments. However, how belowground microbial biodiversity changes along elevational gradient during the growing season is not well understood yet. Here, we investigated the elevational distribution of soil prokaryotic communities by using 16S rRNA amplicon sequencing along an elevational gradient between 3,200 and 4,200 m, and a seasonal gradient between June and September in the Qinghai-Tibetan alpine grasslands. First, we found soil prokaryotic diversity and community composition significantly shifted along the elevational gradient, mainly driven by soil temperature and moisture. Species richness did not show consistent elevational trends, while those of evenness declined with elevation. Copiotrophs and symbiotic diazotrophs declined with elevation, while oligotrophs and AOB increased, affected by temperature. Anaerobic or facultatively anaerobic bacteria and AOA were hump-shaped, mainly influenced by moisture. Second, seasonal patterns of community composition were mainly driven by aboveground biomass, precipitation, and soil temperature. The seasonal dynamics of community composition indicated that soil prokaryotic community, particularly Actinobacteria, was sensitive to short-term climate change, such as the monthly precipitation variation. At last, dispersal limitation consistently dominated the assembly process of soil prokaryotic communities along both elevational and seasonal gradients, especially for those of rare species, while the deterministic process of abundant species was relatively higher at drier sites and in drier July. The balance between deterministic and stochastic processes in abundant subcommunities might be strongly influenced by water conditions (precipitation/moisture). Our findings suggest that both elevation and season can alter the patterns of soil prokaryotic biodiversity in alpine grassland ecosystem of Qinghai-Tibetan Plateau, which is a biodiversity hotspot and is experiencing rapid climate change. This work provides new insights into the response of soil prokaryotic communities to changes in elevation and season, and helps us understand the temporal and spatial variations in such climate change-sensitive regions.

Acidic Media Impedes Tandem Catalysis Reaction Pathways in Electrochemical CO2 Reduction

Electrochemical CO2 reduction (CO2 R) in acidic media with Cu-based catalysts tends to suffer from lowered selectivity towards multicarbon products. This could in principle be mitigated using tandem catalysis, whereby the *CO coverage on Cu is increased by introducing a CO generating catalyst (e.g. Ag) in close proximity. Although this has seen significant success in neutral/alkaline media, here we report that such a strategy becomes impeded in acidic electrolyte. This was investigated through the co-reduction of 13 CO2 /12 CO mixtures using a series of Cu and CuAg catalysts. These experiments provide strong evidence for the occurrence of tandem catalysis in neutral media and its curtailment under acidic conditions. Density functional theory simulations suggest that the presence of H3 O+ weakens the *CO binding energy of Cu, preventing effective utilization of tandem-supplied CO. Our findings also provide other unanticipated insights into the tandem catalysis reaction pathway and important design considerations for effective CO2 R in acidic media.

Microbial carbon use efficiency in different ecosystems: A meta-analysis based on a biogeochemical equilibrium model

Soil microbial carbon use efficiency (CUE) is a crucial parameter that can be used to evaluate the partitioning of soil carbon (C) between microbial growth and respiration. However, general patterns of microbial CUE among terrestrial ecosystems (e.g., farmland, grassland, and forest) remain controversial. To address this knowledge gap, data from 41 study sites (n = 197 soil samples) including 58 farmlands, 95 forests, and 44 grasslands were collected and analyzed to estimate microbial CUEs using a biogeochemical equilibrium model. We also evaluated the metabolic limitations of microbial growth using an enzyme vector model and the drivers of CUE across different ecosystems. The CUEs obtained from soils of farmland, forest, and grassland ecosystems were significantly different with means of 0.39, 0.33, and 0.42, respectively, illustrating that grassland soils exhibited higher microbial C sequestration potentials (p < .05). Microbial metabolic limitations were also distinct in these ecosystems, and carbon limitation was dominant exhibiting strong negative effects on CUE. Exoenzyme stoichiometry played a greater role in impacting CUE values than soil elemental stoichiometry within each ecosystem. Specifically, soil exoenzymatic ratios of C:phosphorus (P) acquisition activities (EEAC:P ) and the exoenzymatic ratio of C:nitrogen (N) acquisition activities (EEAC:N ) imparted strong negative effects on soil microbial CUE in grassland and forest ecosystems, respectively. But in farmland soils, EEAC:P exhibited greater positive effects, showing that resource constraints could regulate microbial resource allocation with discriminating patterns across terrestrial ecosystems. Furthermore, mean annual temperature (MAT) rather than mean annual precipitation (MAP) was a critical climate factor affecting CUE, and soil pH as a major factor remained positive to drive the changes in microbial CUE within ecosystems. This research illustrates a conceptual framework of microbial CUEs in terrestrial ecosystems and provides the theoretical evidence to improve soil microbial C sequestration capacity in response to global change.

Large-scale exploration of nitrogen utilization efficiency in Asia region for rice crop: Variation patterns and determinants

Improving rice nitrogen utilization efficiency (NUtE) is imperative to maximizing future food productivity while minimizing environmental threats, yet knowledge of its variation and the underlying regulatory factors is still lacking. Here, we integrated a dataset with 21,571 data compiled by available data from peer-reviewed literature and a large-scale field survey to address this knowledge gap. The overall results revealed great variations in rice NUtE, which were mainly associated with human activities, climate conditions, and rice variety. Specifically, N supply rate, temperature, and precipitation were the foremost determinants of rice NUtE, and NUtE responses to climatic change differed among rice varieties. Further prediction highlighted the improved rice NUtE with the increasing latitude or longitude. The indica and hybrid rice exhibited higher NUtE in low latitude regions compared to japonica and inbred rice, respectively. Collectively, our results evaluated the primary drivers of rice NUtE variations and predicted the geographic responses of NUtE in different varieties. Linking the global variations in rice NUtE with environmental factors and geographic adaptability provides valuable agronomic and ecological insights into the regulation of rice NUtE.

Childhood-Onset Lupus Nephritis in the Childhood Arthritis and Rheumatology Research Alliance Registry: Short-Term Kidney Status and Variation in Care

OBJECTIVE

The goal was to characterize short-term kidney status and describe variation in early care utilization in a multicenter cohort of patients with childhood-onset systemic lupus erythematosus (cSLE) and nephritis.

METHODS

We analyzed previously collected prospective data from North American patients with cSLE with kidney biopsy-proven nephritis enrolled in the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry from March 2017 through December 2019. We determined the proportion of patients with abnormal kidney status at the most recent registry visit and applied generalized linear mixed models to identify associated factors. We also calculated frequency of medication use, both during induction and ever recorded.

RESULTS

We identified 222 patients with kidney biopsy-proven nephritis, with 64% class III/IV nephritis on initial biopsy. At the most recent registry visit at median (interquartile range) of 17 (8-29) months from initial kidney biopsy, 58 of 106 patients (55%) with available data had abnormal kidney status. This finding was associated with male sex (odds ratio [OR] 3.88, 95% confidence interval [95% CI] 1.21-12.46) and age at cSLE diagnosis (OR 1.23, 95% CI 1.01-1.49). Patients with class IV nephritis were more likely than class III to receive cyclophosphamide and rituximab during induction. There was substantial variation in mycophenolate, cyclophosphamide, and rituximab ever use patterns across rheumatology centers.

CONCLUSION

In this cohort with predominately class III/IV nephritis, male sex and older age at cSLE diagnosis were associated with abnormal short-term kidney status. We also observed substantial variation in contemporary medication use for pediatric lupus nephritis between pediatric rheumatology centers. Additional studies are needed to better understand the impact of this variation on long-term kidney outcomes.

Determining optimal nitrogen management to improve rice yield, quality and nitrogen use efficiency based on multi-index decision analysis method

BACKGROUND

Reasonable nitrogen (N) supply is critical for increasing rice yield while improving grain quality and nitrogen use efficiency (NUE). However, the trade-off relationship between yield, quality and NUE of rice under N management has not been well understood enough. In the present study, a 2-year field experiment was conducted to identify optimal N fertilizer management practices that resulted in high-yield, high-quality and high-NUE by using the technique for order preference by similarity to an ideal solution (TOPSIS) with entropy weight (EW) method.

RESULTS

All the parameters of rice yield, quality and efficiency were remarkably affected by fertilization treatments. Compared with farmer's fertilization practice (FFP), optimizing N fertilizer treatment (OPT) and substituting 20% of N fertilizer with pig manure based on OPT treatment (OPTM) increased grain yield (2.87-6.62%) by maintaining higher 1000-grain weight and filled grains rate. The agronomic NUE (AE) and N partial factor productivity (PFP) under OPT and OPTM treatment were also remarkably increased by 32.81-43.01% and 28.59-33.28% with respect to the value under FFP treatment, respectively. Meanwhile, OPT and OPTM significantly improved the milling quality of rice by increasing brown rice rate (0.71-1.17%) and head rice rate (1.34-2.31%). OPT and OPTM significantly improved appearance quality by decreasing chalkiness and eating quality by reducing amylose content in 2020. The TOPSIS with EW showed that rice comprehensive evaluation could be maintained at a high level under OPT and OPTM.

CONCLUSION

OPT and OPTM were nutrient management modes of high-yield, high-quality and high-efficiency, and promising practice to improve rice comprehensive productivity. This strategy is also highly-consistent with the United Nations Sustainable Development Goals. © 2023 Society of Chemical Industry.

Humoral responses after primary and booster SARS-CoV-2 inactivated vaccination in patients with chronic hepatitis B virus infection: a longitudinal observational study

Given the pandemic of severe acute respiratory syndrome coronavirus 2 Omicron variants, booster vaccination (BV) using inactivated virus vaccines (the third dose) has been implemented in China. However, the immune responses after BV, especially those against Omicron, in patients with chronic hepatitis B virus (HBV) infection (CHB) are unclear. In this prospective longitudinal study, 114 patients with CHB and 68 healthy controls (HCs) were recruited after receiving inactivated vaccination. The anti-receptor-binding domain (RBD) immunoglobulin G (IgG), neutralizing antibodies (NAbs), neutralization against Omicron (BA2.12.1, BA.4/5), and specific B/T cells were evaluated. In patients, anti-RBD IgG was elevated significantly after BV; the titers were as high as those in HCs. Similar results were obtained for the NAbs. However, compared with that against wild type (WT), the neutralization against Omicron was compromised after BV. The frequency of RBD⁺ atypical memory B cells increased, but spike-specific cluster of differentiation 4⁺ /8⁺ T cells remained unchanged after BV. Moreover, no serious adverse events or HBV reactivation were observed after BV. These results suggest that BV significantly enhanced antibody responses against WT; however, it resulted in compromised antibody responses against Omicron in patients with CHB. Hence, new all-in-one vaccines and optimal vaccination strategies should be studied promptly. This article is protected by copyright. All rights reserved.

Swainsonine Induces Liver Inflammation in Mice via Disturbance of Gut Microbiota and Bile Acid Metabolism

Swainsonine induced liver inflammation in livestock; however, the underlying mechanisms, especially the role of bile acids (BAs), in the pathogenesis remained elusive. Here, our results showed that swainsonine induced hepatic inflammation via changing BA metabolism and gut microbiota in mice. Swainsonine significantly upregulated the levels of deoxycholic acid (DCA) and taurine-β-muricholic acid (T-β-MCA) in the serum and liver of mice due to the markedly increased genus Clostridium and the decreased genus Lactobacillus in the gut. As antagonists of the farnesoid X receptor (FXR), elevated DCA and T-β-MCA inhibited hepatic Fxr gene expression and thus suppressed FXR-SHP signaling and activated hepatic Cyp7a1 gene expression, which induced a significant upregulation of the total BA level in serum, contributing to liver inflammation. These findings offer new insights into the underlying mechanisms in which swainsonine induced liver inflammation in mice via the gut-liver axis and suggest that gut microbiota and its metabolite BAs may be underlying triggering factors.

Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants

The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to formally evaluate the hologenome concept. We analyzed the root-endosphere microbiota of two independent watermelon and grapevine plant systems, including ungrafted and reciprocal-grafting combinations. Grafted and ungrafted hosts harbor markedly different microbiota compositions. Furthermore, the results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with interactive effect of both the rootstock and scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.

Risk of waning humoral responses after inactivated or subunit recombinant SARS-CoV-2 vaccination in patients with chronic diseases: Findings from a prospective observational study in China

Heterogeneity of antibody responses has been reported in SARS-CoV-2 vaccination recipients with underlying diseases. We investigated the impact of the presence of comorbidities on the humoral response to SARS-CoV-2 vaccination in patients with chronic disease (PWCD) and assessed the effect of the number of comorbidities on the humoral response to vaccination. In this study, neutralizing antibodies (NAbs) and IgG antibodies against the receptor-binding domain (RBD-IgG) were monitored following a full-course vaccination. In total, 1400 PWCD (82.7%, inactivated vaccines; 17.3%, subunit recombinant vaccine) and 245 healthy controls (65.7% inactivated vaccines, 34.3% subunit recombinant vaccine) vaccinated with inactivated or subunit recombinant SARS-CoV-2 vaccines, were included. The seroconversion and antibody levels of the NAbs and RBD-IgG were different in the PWCD group compared with those in the control group. Chronic hepatitis B (odds ratio [OR]: 0.65; 95% confidence interval [CI]: 0.46-0.93), cancer (OR: 0.65; 95% CI: 0.42-0.99), and diabetes (OR: 0.50; 95% CI: 0.28-0.89) were associated with lower seroconversion of NAbs. Chronic kidney disease (OR: 0.29; 95% CI: 0.11-0.76), cancer (OR: 0.38; 95% CI: 0.23-0.62), and diabetes (OR: 0.37; 95% CI: 0.20-0.69) were associated with lower seroconversion of RBD-IgG. Only the presence of autoimmune disease showed significantly lower NAbs and RBD-IgG titers. Patients with most types of chronic diseases showed similar responses to the controls, but humoral responses were still significantly associated with the presence of ≥2 coexisting diseases. Our study suggested that humoral responses following SARS-CoV-2 vaccination are impaired in patients with certain chronic diseases.

Decreased antibody response to influenza vaccine with an enhanced antibody response to subsequent SARS-CoV-2 vaccination in patients with chronic hepatitis B virus infection

INTRODUCTION

Influenza or SARS-CoV-2 vaccination is especially recommended for people with underlying diseases. For the large number of patients with chronic hepatitis B virus infection (CHB), studies on their immune responses to these vaccines are still lacking.

METHODS

A total of 57 CHB patients and 19 healthy controls (HCs) receiving inactivated influenza vaccination were prospectively followed up. Influenza-specific immunoglobulin G (IgG) antibodies (anti-H1N1, anti-H3N2, and anti-B IgG), antibody-secreting cells (ASCs), and circulating T follicular helper cells were assessed simultaneously. Eight CHB patients subsequently got inactivated SARS-CoV-2 vaccination during 1-year follow-up, and levels of serum antibodies against SARS-CoV-2 were further analyzed.

RESULTS

On day 28 after influenza vaccination, three influenza antibodies levels appeared to be lower in CHB patients than in HCs. And anti-H1N1 IgG level was significantly decreased in cirrhotic patients (p < .05). Anti-H1N1 IgG levels (day 28) were positively correlated with ASC frequencies (day 7) (p < .05), and negatively correlated with cirrhosis and hepatitis B surface antigen levels (p < .05). Anti-SARS-CoV-2 antibodies were higher in patients with influenza vaccination history than in patients without the history (p < .05). Moreover, positive correlations existed between influenza vaccination history and anti-SARS-CoV-2 antibody levels (p < .01).

CONCLUSIONS

CHB patients, especially those with cirrhosis, appeared to have a decreased antibody response to inactivated influenza vaccine. A history of inactivated influenza vaccination within 1 year before inactivated SARS-CoV-2 vaccination might induce stronger anti-SARS-CoV-2 antibody response.

Intraarticular steroids as DMARD-sparing agents for juvenile idiopathic arthritis flares: Analysis of the Childhood Arthritis and Rheumatology Research Alliance Registry

BACKGROUND

Children with juvenile idiopathic arthritis (JIA) who achieve a drug free remission often experience a flare of their disease requiring either intraarticular steroids (IAS) or systemic treatment with disease modifying anti-rheumatic drugs (DMARDs). IAS offer an opportunity to recapture disease control and avoid exposure to side effects from systemic immunosuppression. We examined a cohort of patients treated with IAS after drug free remission and report the probability of restarting systemic treatment within 12 months.

METHODS

We analyzed a cohort of patients from the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry who received IAS for a flare after a period of drug free remission. Historical factors and clinical characteristics and of the patients including data obtained at the time of treatment were analyzed.

RESULTS

We identified 46 patients who met the inclusion criteria. Of those with follow up data available 49% had restarted systemic treatment 6 months after IAS injection and 70% had restarted systemic treatment at 12 months. The proportion of patients with prior use of a biologic DMARD was the only factor that differed between patients who restarted systemic treatment those who did not, both at 6 months (79% vs 35%, p < 0.01) and 12 months (81% vs 33%, p < 0.05).

CONCLUSION

While IAS are an option for all patients who flare after drug free remission, it may not prevent the need to restart systemic treatment. Prior use of a biologic DMARD may predict lack of success for IAS. Those who previously received methotrexate only, on the other hand, are excellent candidates for IAS.

Association between immunosuppressants and poor antibody responses to SARS-CoV-2 vaccines in patients with autoimmune liver diseases

The antibody and B cell responses after inactivated SARS-CoV-2 vaccination have not been well documented in patients with autoimmune liver disease (AILD). Therefore, we conducted a prospective observational study that included AILD patients and healthy participants as controls between July 1, 2021, and September 30, 2021, at the Second Affiliated Hospital of Chongqing Medical University. All adverse events (AEs) after the COVID-19 vaccination were recorded and graded. Immunoglobulin (Ig)-G antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein (anti-RBD-IgG) and neutralizicadng antibodies (NAbs) were tested following full-course vaccination (BBIBP-CorV or CoronaVac). In addition, SARS-CoV-2-specific B cells were detected by flow cytometry. In total, 76 AILD patients and 136 healthy controls (HCs) were included. All AEs were mild and self-limiting, and the incidences were similar between the AILD and HCs. The seropositivity rates of anti-RBD-IgG and NAbs in AILD were 97.4% (100% in HCs, p = 0.13) and 63.2% (84.6% in HCs, p < 0.001), respectively. The titers of anti-RBD-IgG and NAbs were significantly lower in AILD patients than those in HCs. After adjusting for confounders, immunosuppressive therapy was an independent risk factor for low-level anti-RBD-IgG (adjusted odds ratio [aOR]: 4.7; 95% confidence interval [CI], 1.5-15.2; p = 0.01) and a reduced probability of NAbs seropositivity (aOR, 3.0; 95% CI, 1.0-8.9; p = 0.04) in AILD patients. However, regardless of immunosuppressants, the SARS-CoV-2-specific memory B cells responses were comparable between the AILD and HC groups. Our results suggest that inactivated SARS-CoV-2 vaccines (BBIBP-CorV and CoronaVac) are safe, but their immunogenicity is compromised in patients with AILD. Moreover, immunosuppressants are significantly associated with poor antibody responses to the SARS-CoV-2 vaccines. These results could inform physicians and policymakers about decisions on screening the populations at higher risk of poor antibody responses to SARS-CoV-2 vaccines and providing additional vaccinations in patients with AILD.

Rejuvenation of iron oxides enhances carbon sequestration by the 'iron gate' and 'enzyme latch' mechanisms in a rice-wheat cropping system

The 'enzyme latch' theory believes that oxygen constraints on phenol oxidase can restrain the activity of hydrolytic enzymes responsible for decomposition, while the 'iron (Fe) gate' theory suggests that Fe oxidation can decrease phenol oxidase activity and enhance Fe-lignin complexation under oxygen exposure. The objective of this study was to explore the roles of the 'enzyme latch' and 'Fe gate' mechanisms in regulating soil organic carbon (SOC) sequestration in a rice-wheat cropping system subjected to six fertilization treatments: control (CT), chemical fertilizer (CF), CF plus manure (CFM), CF plus straw (CFS), CF plus manure and straw (CFMS), and CF plus organic-inorganic compound fertilizer (OICF). Soil samples were collected after the rice and wheat harvests and wet sieved into large macroaggregates, small macroaggregates, microaggregates, and silt and clay particles. Variations in amorphous and free Fe oxides, Fe-bound organic carbon and phenol oxidase activity were examined. After nine years, compared with the initial soil, the activation degree of free Fe oxides increased by 1.3- to 1.6-fold and the topsoil SOC stock increased by 13-61% across all treatments. Amorphous Fe oxide content, phenol oxidase activity and aggregate mean-weight diameter were higher after the wheat harvest than after the rice harvest. Amorphous Fe oxide content was positively correlated with Fe-bound organic carbon content (P < 0.001) but negatively correlated with phenol oxidase activity (P < 0.001). Therefore, seasonal alternation of wetting and drying can progressively drive the rejuvenation of Fe oxides and simultaneously affect the activity of phenol oxidase. Oxidative precipitation of amorphous Fe oxides promoted the formation of organo-Fe complexes and macroaggregates, while flooding of the paddies decreased the activity of phenol oxidase, thereby resulting in year-round hindered decomposition. Organic fertilization strengthened the roles of the 'Fe gate' and 'enzyme latch' mechanisms, and thus accelerated SOC sequestration in the rice-wheat cropping system.

Identification of alanine aminotransferase 1 interaction network via iTRAQ-based proteomics in alternating migration, invasion, proliferation and apoptosis of HepG2 cells

OBJECTIVE

To investigate the mechanism of alanine aminotransferase 1 (ALT1) in the progression of HCC, the differentially expressed proteins (DEPs) in the ALT1 interaction network were identified by targeted proteomic analysis.

METHODS

Wound healing and transwell assays were conducted to assess the effect of ALT1 on cellular migration and invasion. Cell Counting Kit-8 (CCK-8), colony formation, and flow cytometry assays were performed to identify alterations in proliferation and apoptosis. After coimmunoprecipitation processing, mass spectrometry with iso-baric tags for relative and absolute quantitation was utilized to explore the protein interactions in ALT1 knockdown HepG2 cells.

RESULTS

The results showed that ALT1 knockdown inhibits the migration, invasion, proliferation of HepG2 cells, and promotes apoptosis. A total of 116 DEPs were identified and the bioinformatics analysis suggested that the ALT1-interacting proteins were primarily associated with cellular and metabolic processes. Knockdown of ALT1 in HepG2 cells reduced the expression of Ki67 and epithelial cell adhesion molecule (EP-CAM), while the expression of apoptosis-stimulating protein 2 of p53 (ASPP2) was increased significantly. Suppression of the ALT1 and EP-CAM expression contributed to alterations in epithelial-mesenchymal transition (EMT) -associated markers and matrix metalloproteinases (MMPs). Additionally, inhibition of ALT1 and Ki67 also decreased the expression of apoptosis and proliferation factors. Furthermore, inhibition of ALT1 and ASPP2 also changed the expression of P53, which may be the signaling pathway by which ALT regulates these biological behaviors.

CONCLUSIONS

This study indicated that the ALT1 protein interaction network is associated with the biological behaviors of HepG2 cells via the p53 signaling pathway.

Long-term manure inputs induce a deep selection on agroecosystem soil antibiotic resistome

Although the enrichment of antibiotic resistance genes (ARGs) in diverse organic soils have been explored, understanding of the ecological processes governing the composition of ARGs in long-term organically fertilized soils still remains limited across typical agricultural regions. Thus, the distribution and assembly of ARG profile in three typical agricultural soils (black soil, fluvo-aquic soil, and red soil) under long-term contrasting fertilization regimes (chemical-only vs organic-only) were investigated using high-throughput qPCR (HT-qPCR). The application of organic manure significantly increased the abundance and number of ARGs across soils, as compared to those with chemical fertilizer. Organic manure application enriched the abundance of mobile genetic elements (MGEs), which were positively associated with ARGs. In addition, it is long-term organic fertilizer that enriched the number and abundance of opportunist and specialist ARGs in the fluvo-aquic and red soils, but not black soils. The number and abundance of most generalist ARGs did not change significantly among different fertilization or soil types. The assembly process of the ARG profiles tends to be more deterministic in organically fertilized soils than in chemically fertilized soils. These results suggest that long-term organic fertilizer application may contribute to the persistence and health risk of the soil antibiotic resistomes (especially specialist ARGs).

Safety and antibody response to inactivated COVID-19 vaccine in patients with chronic hepatitis B virus infection

BACKGROUND AND AIMS

The safety and antibody responses of coronavirus disease 2019 (COVID-19) vaccination in patients with chronic hepatitis B (CHB) virus infection is still unclear, and exploration in safety and antibody responses of COVID-19 vaccination in CHB patients is significant in clinical practice.

METHODS

362 adult CHB patients and 87 healthy controls at an interval of at least 21 days after a full-course vaccination (21-105 days) were enrolled. Adverse events (AEs) were collected by questionnaire. The antibody profiles at 1, 2 and 3 months were elucidated by determination of anti-spike IgG, anti-receptor-binding domain (RBD) IgG, and RBD-angiotensin-converting enzyme 2 blocking antibody. SARS-CoV-2 specific B cells were also analysed.

RESULTS

All AEs were mild and self-limiting, and the incidence was similar between CHB patients and controls. Seropositivity rates of three antibodies were similar between CHB patients and healthy controls at 1, 2 and 3 months, but CHB patients had lower titers of three antibodies at 1 month. Compared to healthy controls, HBeAg-positive CHB patients had higher titers of three antibodies at 3 months (all P < .05) and a slower decline in antibody titers. Frequency of RBD-specific B cells was positively correlated with titers of anti-RBD IgG (OR = 1.067, P = .004), while liver cirrhosis, antiviral treatment, levels of HBV DNA, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) and total bilirubin (TB) were not correlated with titers of anti-RBD IgG.

CONCLUSIONS

Inactivated COVID-19 vaccines were well tolerated, and induced effective antibody response against SARS-CoV-2 in CHB patients.

Meta-analysis of diazotrophic signatures across terrestrial ecosystems at the continental scale

Biological nitrogen fixation performed by diazotrophs forms a cornerstone of Earth's terrestrial ecosystem productivity. However, the composition, diversity and distribution of soil diazotrophs are poorly understood across different soil ecosystems. Furthermore, the biological potential of the key diazotroph species in relation to key environmental parameters is unknown. To address this, we used meta-analysis approach to merge together 39 independent diazotroph amplicon sequencing (nifH gene) datasets consisting of 1988 independent soil samples. We then employed multiple statistical analyses and machine-learning approaches to compare diazotroph community differences and indicator species between terrestrial ecosystems on a global scale. The distribution, composition and structure of diazotroph communities varied across seven different terrestrial ecosystems, with community composition exhibiting an especially clear effect. The Cyanobacteria were the most abundant taxa in crust ecosystems (accounting for ~45% of diazotrophs), while other terrestrial ecosystems were dominated by Proteobacteria, including Alpha-, Beta- and Gamma-Proteobacteria (accounting for ~70% of diazotrophs). Farmland ecosystems harboured the highest and crust ecosystems the lowest alpha and phylogenetic diversities. Azospirillum zeae, Skermanella aerolata and four Bradyrhizobium species were identified as key indicator species of potential diazotroph activity. Overall, diazotroph abundances and distribution were affected by multiple environmental parameters, including soil pH, nitrogen, organic carbon, C:N ratio and annual mean precipitation and temperature. Together, our findings suggest that based on the relative abundance and diversity of nifH marker gene, diazotrophs have adapted to a range of environmental niches globally.

Social determinants of health influence disease activity and functional disability in Polyarticular Juvenile Idiopathic Arthritis

BACKGROUND

Social determinants of health (SDH) greatly influence outcomes during the first year of treatment in rheumatoid arthritis, a disease similar to polyarticular juvenile idiopathic arthritis (pJIA). We investigated the correlation of community poverty level and other SDH with the persistence of moderate to severe disease activity and functional disability over the first year of treatment in pJIA patients enrolled in the Childhood Arthritis and Rheumatology Research Alliance Registry.

METHODS

In this cohort study, unadjusted and adjusted generalized linear mixed effects models analyzed the effect of community poverty and other SDH on disease activity, using the clinical Juvenile Arthritis Disease Activity Score-10, and disability, using the Child Health Assessment Questionnaire, measured at baseline, 6, and 12 months.

RESULTS

One thousand six hundred eighty-four patients were identified. High community poverty (≥20% living below the federal poverty level) was associated with increased odds of functional disability (OR 1.82, 95% CI 1.28-2.60) but was not statistically significant after adjustment (aOR 1.23, 95% CI 0.81-1.86) and was not associated with increased disease activity. Non-white race/ethnicity was associated with higher disease activity (aOR 2.48, 95% CI: 1.41-4.36). Lower self-reported household income was associated with higher disease activity and persistent functional disability. Public insurance (aOR 1.56, 95% CI 1.06-2.29) and low family education (aOR 1.89, 95% CI 1.14-3.12) was associated with persistent functional disability.

CONCLUSION

High community poverty level was associated with persistent functional disability in unadjusted analysis but not with persistent moderate to high disease activity. Race/ethnicity and other SDH were associated with persistent disease activity and functional disability.

Interleukin-17A pretreatment attenuates the anti-hepatitis B virus efficacy of interferon-alpha by reducing activation of the interferon-stimulated gene factor 3 transcriptional complex in hepatitis B virus-expressing HepG2 cells

Background

Some cytokine signaling pathways can interact with interferon (IFN)-α pathway and thus regulate cell responses to IFN-α. Levels of the pro-inflammatory cytokine interleukin-17A (IL-17A) were found to be elevated in both the peripheral blood and liver in chronic hepatitis B (CHB) patients. However, how IL-17A affects the anti-HBV activity of IFN-α remains unclear.

Methods

The effects of IL-17A on anti-HBV activity of IFN-α were evaluated in HBV-expressing HepG2 cells (HepG2-HBV1.3) with IL-17A pretreatment and IFN-α stimulation. Culture supernatant levels of HBsAg, HBeAg, and HBV DNA, or intracellular expression of HBsAg and HBcAg were detected by ELISA, real-time quantitative PCR (RT-qPCR), or western blotting (WB). The expression of canonical IFN-α signaling pathway components, including the interferon-α/β receptor (IFNAR), Janus Kinase 1 (JAK1), Tyrosine Kinase 2 (TYK2), the Interferon Stimulated Gene Factor 3 complex (ISGF3) and IFN-stimulated genes (ISGs), was also examined by RT-qPCR, Immunofluorescence or WB. The effects of IL-17A were further investigated by the suppression of the IL-17A pathway with a TRAF6 inhibitor.

Results

Compared to IFN-α stimulation alone, IL-17A pretreatment followed by IFN-α stimulation increased the levels of HBsAg, HBeAg, and HBV DNA, and decreased the levels of ISGF3 complex (phosphorylated (p)-signal transducer and activator of transcription (STAT1)/p-STAT2/IRF9) and antiviral-related ISGs (ISG15, ISG20 and Mx1). Interestingly, IL-17A pretreatment increased the expression of suppressor of cytokine signaling (SOCS) 1, SOCS3 and USP18, which were also the ISGs negatively regulating activity of ISGF3. Moreover, IFNAR1 protein expression declined more sharply in the group with IL-17A pretreatment than in the group with IFN-α stimulation alone. Blocking the IL-17A pathway reversed the effects of IL-17A on the IFN-α-induced activation of ISGF3 and anti-HBV efficacy.

Conclusions

Our results demonstrate that IL-17A pretreatment could attenuate IFN-α-induced anti-HBV activity by upregulating negative regulators of the critical transcriptional ISGF3 complex. Thus, this might be a potential target for improving response to IFN-α therapy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01753-x.

Rare Bacteria Assembly in Soils Is Mainly Driven by Deterministic Processes

Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules.

A panel of urine-derived biomarkers to identify sepsis and distinguish it from systemic inflammatory response syndrome

Sepsis is a potentially fatal condition caused by infection. It is frequently difficult to distinguish sepsis from systemic inflammatory response syndrome (SIRS), often resulting in poor prognoses and the misuse of antibiotics. Hence, highly sensitive and specific biomarkers are needed to differentiate sepsis from SIRS. Urine samples were collected and segregated by group (a sepsis group, a SIRS group, and a healthy control group). iTRAQ was used to identify the differentially expressed proteins among the three groups. The identified proteins were measured by ELISA in urine samples. Finally, all the acquired data were analyzed in SPSS. C-reactive protein, leucine-rich alpha glycoprotein-1 and serum amyloid A (SAA) protein were differentially expressed among the three groups. The adjusted median concentrations of urinary C-reactive protein were 1337.6, 358.7, and 2.4 in the sepsis, SIRS, and healthy control groups, respectively. The urinary leucine-rich alpha glycoprotein-1 levels in these three groups were 1614.4, 644.5, and 13.6, respectively, and the levels of SAA were 6.3, 2.9, and 0.07, respectively. For all three of these measures, the sepsis group had higher levels than the SIRS group (P < 0.001), and the SIRS group had higher levels than the healthy control group. When combined, the three biomarkers had a sensitivity of 0.906 and a specificity of 0.896 in distinguishing sepsis from SIRS. Urinary C-reactive protein, urinary leucine-rich alpha glycoprotein-1 and urinary SAA have diagnostic value in cases of sepsis. This initial study suggests the possibility of improved differential diagnosis between sepsis and systemic inflammatory response syndrome; additional confirmation is necessary to corroborate the findings.

Microbial generalist or specialist: Intraspecific variation and dormancy potential matter

Microbial generalists and specialists coexist in the soil environment while having distinctive impacts on microbial community dynamics. In microbial ecology, the underlying mechanisms as to why a species is a generalist or a specialist remain ambiguous. Herein, we collected soils across a national scale and identified bacterial generalists and specialists according to niche breadth at the species level (OTU level), and the single-nucleotide differences in each species were measured to investigate intraspecific variation (at zero-radius OTU level). Compared with that of the specialists, the intraspecific variation of the generalists was much higher, which ensured their wider niche breadth and lower variability. The higher asynchrony and different niche preferences of conspecific individuals and the higher dormancy potential within the generalists further contributed to their stability in varying environments. Besides, generalists were less controlled by environmental filtering, which was indicated by the stronger signature of stochastic processes in their assembly, and had higher diversification and transition rates that allowed them to adapt to environmental changes to a greater extent than specialists. Overall, this study provides a new comprehensive understanding of the rules of assembly and the evolutionary roles of bacterial generalists and specialists. It also highlights the importance of intraspecific variation and the dormancy potential in the stability of species.

Manipulating the soil microbiomes during a community recovery process with plant beneficial species for the suppression of Fusarium wilt of watermelon

Fusarium wilt is a devastating disease which impacts watermelon production. Soil fumigation using dazomet followed by biological organic fertilizer was applied to suppress the Fusarium wilt disease. We propose that fumigation suppresses the soil indigenous community, especially the soil-borne pathogens, while the utilization of bio-organic fertilizer facilitates the recovery of the soil microbiome to a beneficial, suppressive state through the introduction of plant growth-promoting microorganisms. Greenhouse experiment showed that applied biological organic fertilizer after dazomet fumigation effective restrain the disease incidence with a 93.6% disease control. Fumigation strongly decreased soil microbial diversity and altered relative taxa abundances, suggesting the possibility of niche release by the resident soil microbial community. Fumigation followed by bio-fertilizer transformed the soil microbial community composition and resulted in higher relative abundances of beneficial microbial groups such as Bacillus (8.5%) and Trichoderma (13.5%), coupled with lower Fusarium abundance compared to other treatments. Network analysis illustrated that soil fumigation decreased interactions within the soil microbial community with less nodes and links while bio-fertilizer addition promoted node interactions. In addition, bio-fertilizer addition after fumigation resulted in the beneficial species becoming the key network connectors. Collectively, fumigation appears to release the resident soil niche resulting in lower diversity while the beneficial microbes introduced by bio-fertilizer addition colonize these niches, leading to a more complex community with fewer pathogens that suppresses Fusarium wilt disease incidence.

Seed-borne, endospheric and rhizospheric core microbiota as predictors of plant functional traits across rice cultivars are dominated by deterministic processes

A host-plant and its associated microbiota depend on one another. However, the assembly process and the functioning of host-associated microbiota are poorly understood. Herein, rice was used as model plant to investigate the assemblage of bacterial microbiota, including those in the seed, root endosphere and rhizosphere. We also assessed the degree to which endosphere and rhizosphere communities were influenced by vertical transmission through seed and identified the core microbes that potentially associated with plant phenotypic properties. Plant microhabitat, rather than subspecies type, was the major driver shaping plant-associated bacterial microbiota. Deterministic processes were primarily responsible for community assembly in all microhabitats. The influence of vertical transmission from seed to root-associated bacterial communities appeared to be quite weak (endosphere) or even absent (rhizosphere). A core microbial community composed of 15 generalist species persisted across different microhabitats and represented key connectors in networks. Host-plant functional traits were linked to the relative abundance of these generalist core microbes and could be predicted from them using machine learning algorithms. Overall, bacterial microbiota is assembled by host-plant interactions in a deterministic-based manner. This study enhances our understanding of the driving mechanisms and associations of microbiota in various plant microhabitats and provides new perspectives to improve plant performance.

Harnessing Thermoelectric Puddles via the Stacking Order and Electronic Screening in Graphene

Thermoelectricity has been investigated mostly on the macroscopic scale despite the fact that its origin is linked to the local electronic band structure of materials. While the role of thermopower from microscopic structures (e.g., surfaces or grain boundaries) increases for emerging thermoelectric materials, manipulating thermoelectric puddles, spatially varying levels of thermoelectric power on the nanometer scale, remains unexplored. Here, we illustrate thermoelectric puddles that can be harnessed via the stacking order and electronic screening in graphene. The local thermoelectric elements were investigated by gate-tunable scanning thermoelectric microscopy on the atomic scale, revealing the roles of local lattice symmetry, impurity charge scatterings, and mechanical strains in the thermopower system. The long-range screening of electrons at the Dirac point in graphene, which could be reached by in-operando spectroscopy, allowed us to unveil distinct thermoelectric puddles in the graphene that are susceptible to the stacking order and external strain. Thus, manipulating thermoelectric puddles via a lattice symmetry and electronic engineering will realize practical thermopower systems with low-dimensional materials.

Structural Engineering of Ultrathin ReS2 on Hierarchically Architectured Graphene for Enhanced Oxygen Reduction

Herein, binary heteronanosheets made of ultrathin ReS₂ nanosheets and reduced graphene oxide (RGO) with either a two-dimensional (2D) "sheet-on-sheet" architecture (2D ReS₂/RGO) or a three-dimensional hierarchical structure (3D ReS₂/RGO) are constructed through rational structure-engineering strategies. In the resultant 3D ReS₂/RGO heteronanosheets, the ultrathin ReS₂ nanosheets are bridged on the RGO surface through Re-O bonds in a vertically oriented manner, which endows the heteronanosheets with open frameworks and a hierarchical porous structure. In sharp contrast to the 2D ReS₂/RGO, the 3D ReS₂/RGO heteronanosheets are featured with abundant active sites and channels for efficient electrolyte ions transport. This, coupled with the strong affinity toward oxygen-containing intermediates intrinsically associated with the binary ReS₂/RGO structure, imparts excellent oxygen reduction performance to the 3D ReS₂/RGO heteronanosheets for potential applications in fuel cells and metal-air batteries.

Multifaceted Interaction Between Hepatitis B Virus Infection and Lipid Metabolism in Hepatocytes: A Potential Target of Antiviral Therapy for Chronic Hepatitis B

Hepatitis B virus (HBV) is considered a “metabolic virus” and affects many hepatic metabolic pathways. However, how HBV affects lipid metabolism in hepatocytes remains uncertain yet. Accumulating clinical studies suggested that compared to non-HBV-infected controls, chronic HBV infection was associated with lower levels of serum total cholesterol and triglycerides and a lower prevalence of hepatic steatosis. In patients with chronic HBV infection, high ALT level, high body mass index, male gender, or old age was found to be positively correlated with hepatic steatosis. Furthermore, mechanisms of how HBV infection affected hepatic lipid metabolism had also been explored in a number of studies based on cell lines and mouse models. These results demonstrated that HBV replication or expression induced extensive and diverse changes in hepatic lipid metabolism, by not only activating expression of some critical lipogenesis and cholesterolgenesis-related proteins but also upregulating fatty acid oxidation and bile acid synthesis. Moreover, increasing studies found some potential targets to inhibit HBV replication or expression by decreasing or enhancing certain lipid metabolism-related proteins or metabolites. Therefore, in this article, we comprehensively reviewed these publications and revealed the connections between clinical observations and experimental findings to better understand the interaction between hepatic lipid metabolism and HBV infection. However, the available data are far from conclusive, and there is still a long way to go before clarifying the complex interaction between HBV infection and hepatic lipid metabolism.

Mitrofanovite, Layered Platinum Telluride, for Active Hydrogen Evolution

Two-dimensional (2D) layered catalysts have been considered as a class of ideal catalysts for hydrogen evolution reaction (HER) because of their abundant active sites with almost zero Gibbs energy change for hydrogen adsorption. Despite the promising performance, the design of stable and economic electrochemical catalyst based on 2D materials remains to be resolved for industrial-scale hydrogen production. Here, we report layered platinum tellurides, mitrofanovite Pt₃Te₄, which serves as an efficient and stable catalyst for HER with an overpotential of 39.6 mV and a Tafel slope of 32.7 mV/dec together with a high current density exceeding 7000 mA/cm². Pt₃Te₄ was synthesized as nanocrystals on a metallic molybdenum ditelluride (MoTe₂) template by a rapid electrochemical method. X-ray diffraction and high-resolution transmission microscopy revealed that the Pt₃Te₄ nanocrystals have a unique layered structure with repeated monolayer units of PtTe and PtTe₂. Theoretical calculations exhibit that Pt₃Te₄ with numerous edges shows near-zero Gibbs free-energy change of hydrogen adsorption, which shows the excellent HER performance as well as the extremely large exchange current density for massive hydrogen production.

Dynamics of the antibiotic resistome in agricultural soils amended with different sources of animal manures over three consecutive years

The application of animal manure is generally considered an important transmission pathway for antibiotic resistance genes (ARGs) in soil. Nevertheless, the fate of ARGs in soil where manure from different sources has been repeatedly implemented is not fully understood. Thus, the succession of ARGs and bacterial communities following the repeated application of three types of animal manures (pig, chicken, and cow manure) to agricultural soil were investigated using Illumina sequencing analysis and high-throughput qPCR. Results showed that manure application remarkably increased the abundance of soil ARGs by increasing the enrichment of indigenous ARGs and introducing extrinsic ARGs. There were no prominent differences in the abundance or diversity of ARGs among the three different manured soils. The abundance and diversity of ARGs in manured soils increased over three consecutive years. Additionally, the abundance of mobile gene elements (MGEs) and bacteria were positively correlated with ARGs, while the changes in the ARG profiles were dramatically associated with the MGEs and bacterial communities. These findings imply that repeated manure application may facilitate to the accumulation and persistence of the soil resistome by regulation of the bacterial community and horizontal gene transfer, providing better insights into the temporal dynamics of soil ARGs in agro-ecosystems.

Anatomically induced changes in rice leaf mesophyll conductance explain the variation in photosynthetic nitrogen use efficiency under contrasting nitrogen supply

BACKGROUND

The ratio of CO₂ mesophyll conductance (g_m) to Ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) content has been suggested to positively affect photosynthetic nitrogen use efficiency (PNUE). The anatomical basis of g_m has been quantified, but information on the relationship between cell-level anatomies and PNUE is less advanced. Here, hydroponic experiments were conducted in rice plants supplied with ammonium (NH₄⁺) and nitrate (NO₃^-) under three N levels (low, 0.71 mM; intermediate, 2.86 mM; high, 7.14 mM) to investigate the gas exchange parameters, leaf anatomical structure and PNUE.

RESULTS

The results showed a lower PNUE in plants supplied with high nitrogen and NH₄⁺, which was positively correlated with the g_m/Rubisco ratio. A one-dimensional within-leaf model revealed that the resistance to CO₂ diffusion in the liquid phase (r_liq) dominated the overall mesophyll resistance (r_m), in which CO₂ transfer resistance in the cell wall, cytoplasm and stroma were significantly affected by nitrogen supply. The chloroplast surface area exposed to intercellular space (S_c) per Rubisco rather than the g_m/S_c ratio was positively correlated with PNUE and was thus considered a key component influencing PNUE.

CONCLUSION

In conclusion, our study emphasized that S_c was the most important anatomical trait in coordinating g_m and PNUE with contrasting N supply.

Plant Grafting Shapes Complexity and Co-occurrence of Rhizobacterial Assemblages

Grafting is a basic technique which is widely used to increase yield and enhance biotic and abiotic stress tolerance in plant production. The diversity and interactions of rhizobacterial assemblages shaped by grafting are important for the growth of their hosts but remain poorly understood. To test the hypothesis that plant grafting shapes complexity and co-occurrence of rhizobacterial assemblage, four types of plants, including ungrafted bottle gourd (B), ungrafted watermelon (W), grafted watermelon with bottle gourd rootstock (W/B), and grafted bottle gourd with watermelon rootstock (B/W), were cultivated in two soil types in a greenhouse, and the rhizosphere bacterial communities were analyzed by 16S rRNA gene high-throughput sequencing. Both the soil type and grafting significantly influenced the bacterial community composition. Grafting increased bacterial within-sample diversity in both soils. Core enriched operational taxonomic units (OTUs) in the W/B rhizosphere compared with the other three treatments (B, W, and B/W) were mainly affiliated with Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which are likely related to methanol oxidation, methylotrophy, fermentation, and ureolysis. Co-occurrence network analysis proved that grafting increased network complexity, including the number of nodes, edges, and modules. Moreover, grafting strengthened the structural robustness of the network in the rhizosphere, while ungrafted watermelon had the lowest network robustness. Homogeneous selection played a predominant role in bacterial community assembly, and the contribution of dispersal limitation was increased in grafted watermelon with bottle gourd rootstock. Grafting increased the diversity and transformed the network topology of the bacterial community, which indicated that grafting could improve species coexistence in the watermelon rhizosphere.

Critical transition of soil bacterial diversity and composition triggered by nitrogen enrichment

Soil bacterial communities are pivotal in regulating terrestrial biogeochemical cycles and ecosystem functions. The increase in global nitrogen (N) deposition has impacted various aspects of terrestrial ecosystems, but we still have a rudimentary understanding of whether there is a threshold for N input level beyond which soil bacterial communities will experience critical transitions. Using high-throughput sequencing of the 16S rRNA gene, we examined soil bacterial responses to a long-term (13 yr), multi-level, N addition experiment in a temperate steppe of northern China. We found that plant diversity decreased in a linear fashion with increasing N addition. However, bacterial diversity responded nonlinearly to N addition, such that it was unaffected by N input below 16 g N·m^-2 ·yr^-1 , but decreased substantially when N input exceeded 32 g N·m^-2 ·yr^-1 . A meta-analysis across four N addition experiments in the same study region further confirmed this nonlinear response of bacterial diversity to N inputs. Substantial changes in soil bacterial community structure also occurred between N input levels of 16 to 32 g N·m^-2 ·yr^-1 . Further analysis revealed that the loss of soil bacterial diversity was primarily attributed to the reduction in soil pH, whereas changes in soil bacterial community were driven by the combination of increased N availability, reduced soil pH, and changes in plant community structure. In addition, we found that N addition shifted bacterial communities toward more putatively copiotrophic taxa. Overall, our study identified a threshold of N input level for bacterial diversity and community composition. The nonlinear response of bacterial diversity to N input observed in our study indicates that although bacterial communities are resistant to low levels of N input, further increase in N input could trigger a critical transition, shifting bacterial communities to a low-diversity state.

Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes

In the processes controlling ecosystem fertility, fungi are increasingly acknowledged as key drivers. However, our understanding of the rules behind fungal community assembly regarding the effect of soil fertility level remains limited. Using soil samples from typical tea plantations spanning c. 2167 km north-east to south-west across China, we investigated the assemblage complexity and assembly processes of 140 fungal communities along a soil fertility gradient. The community dissimilarities of total fungi and fungal functional guilds increased with increasing soil fertility index dissimilarity. The symbiotrophs were more sensitive to variations in soil fertility compared with pathotrophs and saprotrophs. Fungal networks were larger and showed higher connectivity as well as greater potential for inter-module connection in more fertile soils. Environmental factors had a slightly greater influence on fungal community composition than spatial factors. Species abundance fitted the Zipf-Mandelbrot distribution (niche-based mechanisms), which provided evidence for deterministic-based processes. Overall, the soil fungal communities in tea plantations responded in a deterministic manner to soil fertility, with high fertility correlated with complex fungal community assemblages. This study provides new insights that might contribute to predictions of fungal community complexity.