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The continuous increase of the greenhouse gas nitrous oxide (N2O) in the atmosphere due to increasing anthropogenic nitrogen input in agriculture has become a global concern. In recent years, identification of the microbial assemblages responsible for soil N2O production has substantially advanced with the development of molecular technologies and the discoveries of novel functional guilds and new types of metabolism. However, few practical tools are available to effectively reduce in situ soil N2O flux. Combating the negative impacts of increasing N2O fluxes poses considerable challenges and will be ineffective without successfully incorporating microbially regulated N2O processes into ecosystem modeling and mitigation strategies. Here, we synthesize the latest knowledge of (i) the key microbial pathways regulating N2O production and consumption processes in terrestrial ecosystems and the critical environmental factors influencing their occurrence, and (ii) the relative contributions of major biological pathways to soil N2O emissions by analyzing available natural isotopic signatures of N2O and by using stable isotope enrichment and inhibition techniques. We argue that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling in order to increase the estimation reliability of N2O emissions. We further propose a molecular methodology oriented framework from gene to ecosystem scales for more robust prediction and mitigation of future N2O emissions. This review summarizes the major microbial pathways of soil N2O production, and key environmental factors modulating their relative contributions, and further proposes to use a combination of state-of-the-art approaches for better source partitioning and incorporation of microbial datasets to achieve better predictive ecosystem models.

Purpose Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, is a pivotal component of the biogeochemical nitrogen cycle. Nitrification was conventionally assumed as a two-step process in which ammonia oxidation was thought to be catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nitrite oxidation by nitrite-oxidizing bacteria (NOB). This long-held assumption of labour division between the two functional groups, however, was challenged by the recent unexpected discovery of complete ammonia oxidizers within the Nitrospira genus that are capable of converting ammonia to nitrate in a single organism (comammox). This breakthrough raised fundamental questions on the niche specialization and differentiation of comammox organisms with other canonical nitrifying prokaryotes in terrestrial ecosystems. Materials and methods This article provides an overview of the recent insights into the genomic analysis, physiological characterization and environmental investigation of the comammox organisms, which have dramatically changed our perspective on the aerobic nitrification process. By using quantitative PCR analysis, we also compared the abundances of comammox Nitrospira clade A and clade B, AOA, AOB and NOB in 300 forest soil samples from China spanning a wide range of soil pH. Results and discussion Comammox Nitrospira are environmentally widespread and numerically abundant in natural and engineered habitats. Physiological data, including ammonia oxidation kinetics and metabolic versatility, and comparative genomic analysis revealed that comammox organisms might functionally outcompete other canonical nitrifiers under highly oligotrophic conditions. These findings highlight the necessity in future studies to re-evaluate the niche differentiation between ammonia oxidizers and their relative contribution to nitrification in various terrestrial ecosystems by including comammox Nitrospira in such comparisons. Conclusions The discovery of comammox and their broad environmental distribution added a new dimension to our knowledge of the biochemistry and physiology of nitrification and has far-reaching implications for refined strategies to manipulate nitrification in terrestrial ecosystems and to maximize agricultural productivity and sustainability.

Human infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) and there is no cure currently. The 3CL protease (3CLpro) is a highly conserved protease which is indispensable for CoVs replication, and is a promising target for development of broad-spectrum antiviral drugs. In this study we investigated the anti-SARS-CoV-2 potential of Shuanghuanglian preparation, a Chinese traditional patent medicine with a long history for treating respiratory tract infection in China. We showed that either the oral liquid of Shuanghuanglian, the lyophilized powder of Shuanghuanglian for injection or their bioactive components dose-dependently inhibited SARS-CoV-2 3CLpro as well as the replication of SARS-CoV-2 in Vero E6 cells. Baicalin and baicalein, two ingredients of Shuanghuanglian, were characterized as the first noncovalent, nonpeptidomimetic inhibitors of SARS-CoV-2 3CLpro and exhibited potent antiviral activities in a cell-based system. Remarkably, the binding mode of baicalein with SARS-CoV-2 3CLpro determined by X-ray protein crystallography was distinctly different from those of known 3CLpro inhibitors. Baicalein was productively ensconced in the core of the substrate-binding pocket by interacting with two catalytic residues, the crucial S1/S2 subsites and the oxyanion loop, acting as a “shield” in front of the catalytic dyad to effectively prevent substrate access to the catalytic dyad within the active site. Overall, this study provides an example for exploring the in vitro potency of Chinese traditional patent medicines and effectively identifying bioactive ingredients toward a specific target, and gains evidence supporting the in vivo studies of Shuanghuanglian oral liquid as well as two natural products for COVID-19 treatment.

PurposeTo develop an ultrasound (US)-based radiomics score for preoperative prediction of microvascular invasion (MVI) in hepatocellular carcinoma (HCC).MethodsBetween January 1, 2012, and October 31, 2017, a total of 482 HCC patients who underwent contrast-enhanced ultrasound (CEUS) were retrospectively reviewed. The study population was divided into a training cohort (n = 341) and a validation cohort (n = 141) based on a cutoff time of January 1, 2016. Radiomics features were extracted from the grayscale US images of HCC. After features selection, a radiomics score was developed from the training cohort. The incremental value of the radiomics score to the clinic-pathological factors for MVI prediction was assessed in the validation cohort with respect to discrimination, calibration, and clinical usefulness.ResultsThe US-based radiomics score consisted of six selected features. Multivariate logistic regression analysis showed that the radiomics score, alpha-fetoprotein (AFP), and tumor size were independent predictors of MVI. The radiomics nomogram (based on the three factors) showed better performance for MVI detection (area under the curve [AUC] 0.731[0.647, 0.815] than the clinical nomogram (based on AFP and tumor size) (0.634 [0.543, 0.724]) (p = 0.015). Both nomograms showed good calibration. Decision curve analysis demonstrated that in terms of clinical usefulness, the radiomics nomogram outperformed the clinical nomogram.ConclusionThe US-based radiomics score was an independent predictor of MVI in HCC. Combining the radiomics score with clinical factors improved the prediction efficacy.Key points• Radiomics can be applied in US images.• US-based radiomics score was an independent predictor of MVI.• Radiomics nomogram incorporated with the radiomics score showed good performance for MVI prediction.

Mass spectrometry imaging (MSI) is a powerful analytical technique that generates maps of hundreds of molecules in biological samples with high sensitivity and molecular specificity. Advanced MSI platforms with capability of high‐spatial resolution and high‐throughput acquisition generate vast amount of data, which necessitates the development of computational tools for MSI data analysis. In addition, computation‐driven MSI experiments have recently emerged as enabling technologies for further improving the MSI capabilities with little or no hardware modification. This review provides a critical summary of computational methods and resources developed for MSI data analysis and interpretation along with computational approaches for improving throughput and molecular coverage in MSI experiments. This review is focused on the recently developed artificial intelligence methods and provides an outlook for a future paradigm shift in MSI with transformative computational methods. Computational methods play a key role in mass spectrometry imaging (MSI) by enabling both efficient data analysis and data driven MSI experiments. A concise overview of emerging artificial intelligence methods in MSI provided herein describes challenges associated with the development of these approaches and provides an outlook for a future paradigm shift in MSI enabled by transformative computational methods.

Solar‐to‐hydrogen conversion based on photocatalytic water splitting is a promising pathway for sustainable hydrogen production. The photocatalytic process requires highly active, inexpensive, and earth‐abundant materials as photocatalysts. As a presentative layer‐structured transition metal dichalcogenides, molybdenum disulfide (MoS2) is attracting intensive attention due to its unique electro and photo properties. In this article, we comprehensively review the recent research efforts of exploring MoS2 as a co‐catalyst for photocatalytic hydrogen production from water, with emphasis on its combination with CdS, CdSe, graphene, carbon nitride, TiO2, and others. It is shown that MoS2–semiconductor composites are promising photocatalysts for hydrogen evolution from water under visible light irradiation. This article comprehensively reviews the recent research efforts of exploring MoS2 as a co‐catalyst for photocatalytic hydrogen production from water.

The role of soil biodiversity in regulating multiple ecosystem functions is poorly understood, limiting our ability to predict how soil biodiversity loss might affect human wellbeing and ecosystem sustainability. Here, combining a global observational study with an experimental microcosm study, we provide evidence that soil biodiversity (bacteria, fungi, protists and invertebrates) is significantly and positively associated with multiple ecosystem functions. These functions include nutrient cycling, decomposition, plant production, and reduced potential for pathogenicity and belowground biological warfare. Our findings also reveal the context dependency of such relationships and the importance of the connectedness, biodiversity and nature of the globally distributed dominant phylotypes within the soil network in maintaining multiple functions. Moreover, our results suggest that the positive association between plant diversity and multifunctionality across biomes is indirectly driven by soil biodiversity. Together, our results provide insights into the importance of soil biodiversity for maintaining soil functionality locally and across biomes, as well as providing strong support for the inclusion of soil biodiversity in conservation and management programmes. Combining field data from 83 sites on five continents, together with microcosm experiments, the authors show that nutrient cycling, decomposition, plant production and other ecosystem functions are positively associated with a higher diversity of a wide range of soil organisms.

Summary It is a grand challenge to ensure the food security for a predicted world population of exceeding 9.7 billion by 2050, especially in an era of global climate change, land degradation and biodiversity loss. Current agricultural productions are mainly relying on synthetic chemical fertilisers to boost plant productivity but have undesirable effects on the environment and soil biodiversity. A promising direction in sustainable agriculture is to harness naturally occurring processes of beneficial plant‐associated microbiomes to ensure sustained crop production and global food security. Despite the significant progress made in the development of beneficial microbes as inoculants to enhance plant performance, challenges remain with the translation of knowledge of plant and soil microbiomes to successful microbial products in the agricultural sector. Here, we highlight how fertilizer technology should be renovated by harnessing microbiome‐based innovations to promote plant productivity and contribute to the end of hunger. Conceptual diagrams to harness the plant‐microbe interactions for the development of new microbial products to improve plant performance. We propose to identify the core group of crop‐specific plant signalling molecules under various environmental stresses, and to extract the selected signalling molecules with the capacity to promote activities of beneficial microbes in the rhizosphere. The high‐throughput isolation approach can be used to isolate plant beneficial microbes in a high‐throughput manner, and the isolated bacterial cultures can be used to create various synthetic communities to test their effects on plant performance in controlled and field experiments.

Two typical processes have been developed for the conversion of methane and carbon dioxide to higher valuable products: dry reforming of methane (DRM) and CO2‐oxidative coupling of methane (CO2‐OCM). Numerous articles reviewed progresses in either DRM or CO2‐OCM, but no one covers both processes. In this review article, we systematically evaluated progresses in both DRM and CO2‐OCM processes for conversion of methane and CO2 to highly valuable products. Critical issues, which are carbon deposition and high energy cost for DRM and the contradiction between large activity and high selectivity for CO2‐OCM, were emphasized. Strategies to develop effective catalysts were evaluated, including the enhancement of metal‐support interactions, the introduction of promotors, the formation of solid solutions, and the construction of core‐shell structures. Plasma and photocatalysis were discussed as new promising technologies for DRM and CO2‐OCM. Dry reforming of methane (DRM) and CO2‐oxidative coupling of methane (CO2‐OCM) are the two typical processes for the conversion of methane and carbon dioxide to higher valuable products. This review article systematically evaluated progresses in both DRM and CO2‐OCM processes.

Understanding how antibiotic resistance emerges and evolves in natural habitats is critical for predicting and mitigating antibiotic resistance in the context of global change. Bacteria have evolved antibiotic production as a strategy to fight competitors, predators and other stressors, but how predation pressure of their most important consumers (i.e., protists) affects soil antibiotic resistance genes (ARGs) profiles is still poorly understood. To address this gap, we investigated responses of soil resistome to varying levels of protistan predation by inoculating low, medium and high concentrations of indigenous soil protist suspensions in soil microcosms. We found that an increase in protistan predation pressure was strongly associated with higher abundance and diversity of soil ARGs. High protist concentrations significantly enhanced the abundances of ARGs encoding multidrug ( oprJ and ttgB genes) and tetracycline ( tetV) efflux pump by 608%, 724% and 3052%, respectively. Additionally, we observed an increase in the abundance of numerous bacterial genera under high protistan pressure. Our findings provide empirical evidence that protistan predation significantly promotes antibiotic resistance in soil bacterial communities and advances our understanding of the biological driving forces behind the evolution and development of environmental antibiotic resistance.