Relative importance between nitrification and denitrification to N2 O from a global perspective.

Nitrous oxide (N2 O) is a potent greenhouse gas, and its mitigation is a pressing task in the coming decade. However, it remains unclear which specific process between concurrent nitrification and denitrification dominates worldwide N2 O emission. We snagged an opportunity to ascertain whence the N2 O came and which were the controlling factors on the basis of 1315 soil N2 O observations from 74 peer-reviewed articles. The average N2 O emission derived from nitrification (N2 On ) was higher than that from denitrification (N2 Od ) worldwide. The ratios of nitrification-derived N2 O to denitrification-derived N2 O, hereof N2 On :N2 Od , exhibited large variations across terrestrial ecosystems. Although soil carbon and nitrogen content, pH, moisture, and clay content accounted for a part of the geographical variations in the N2 On :N2 Od ratio, ammonia-oxidizing microorganisms (AOM):denitrifier ratio was the pivotal driver for the N2 On :N2 Od ratios, since the AOM:denitrfier ratio accounted for 53.7% of geographical variations in N2 On :N2 Od ratios. Compared with natural ecosystems, soil pH exerted a more remarkable role to dictate the N2 On :N2 Od ratio in croplands. This study emphasizes the vital role of functional soil microorganisms in geographical variations of N2 On :N2 Od ratio and lays the foundation for the incorporation of soil AOM:denitrfier ratio into models to better predict N2 On :N2 Od ratio. Identifying soil N2 O derivation will provide a global potential benchmark for N2 O mitigation by manipulating the nitrification or denitrification.

Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum.

Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.

Global variations and controlling factors of anammox rates.

Soil anammox is an environmentally friendly way to eliminate reactive nitrogen (N) without generating nitrous oxide. Nevertheless, the current earth system models have not incorporated the anammox due to the lack of parameters in anammox rates on a global scale, limiting the accurate projection for N cycling. A global synthesis with 1212 observations from 89 peer-reviewed papers showed that the average anammox rate was 1.60 ± 0.17 nmol N g-1 h-1 in terrestrial ecosystems, with significant variations across different ecosystems. Wetlands exhibited the highest rate (2.17 ± 0.31 nmol N g-1 h-1 ), followed by croplands at 1.02 ± 0.09 nmol N g-1 h-1 . The lowest anammox rates were observed in forests and grasslands. The anammox rates were positively correlated with the mean annual temperature, mean annual precipitation, soil moisture, organic carbon (C), total N, as well as nitrite and ammonium concentrations, but negatively with the soil C:N ratio. Structural equation models revealed that the geographical variations in anammox rates were primarily influenced by the N contents (such as nitrite and ammonium) and abundance of anammox bacteria, which collectively accounted for 42% of the observed variance. Furthermore, the abundance of anammox bacteria was well simulated by the mean annual precipitation, soil moisture, and ammonium concentrations, and 51% variance of the anammox bacteria was accounted for. The key controlling factors for soil anammox rates differed from ecosystem type, for example, organic C, total N, and ammonium contents in croplands, versus soil C:N ratio and nitrite concentrations in wetlands. The controlling factors in soil anammox rate identified by this study are useful to construct an accurate anammox module for N cycling in earth system models.

Distinct patterns of soil bacterial and fungal community assemblages in subtropical forest ecosystems under warming.

Climate change globally affects soil microbial community assembly across ecosystems. However, little is known about the impact of warming on the structure of soil microbial communities or underlying mechanisms that shape microbial community composition in subtropical forest ecosystems. To address this gap, we utilized natural variation in temperature via an altitudinal gradient to simulate ecosystem warming. After 6 years, microbial co-occurrence network complexity increased with warming, and changes in their taxonomic composition were asynchronous, likely due to contrasting community assembly processes. We found that while stochastic processes were drivers of bacterial community composition, warming led to a shift from stochastic to deterministic drivers in dry season. Structural equation modelling highlighted that soil temperature and water content positively influenced soil microbial communities during dry season and negatively during wet season. These results facilitate our understanding of the response of soil microbial communities to climate warming and may improve predictions of ecosystem function of soil microbes in subtropical forests.

Exploring the repairing mechanisms of reduced graphene oxide (rGo) on the dysregulation of Xenopus Laevis larva hypothalamus-pituitary-thyroid (HPT) axis caused by chiral triazole fungicide metconazole.

Replacing chair fungicide racemate marketed product by its enantiomer with high activity and low environmental risk for application is a more environmentally friendly methods to control crop diseases. Moreover, carbon-based nanomaterials, with the desirable chemical and mechanical properties, exhibits latent reduce fungicide toxicity capability, while the mechanism is still poorly understood. Therefore, the present study characterized the toxicity of rac-metconazole (Mez; (1RS,5RS;1RS,5SR)-5-(4-chlorobenzyl)-2,2-dimethyl-1-(1H)) and its two cis-enantiomers as well as the repairing effect of reduced graphene oxide (rGo) on Xenopus Laevis larva by examining growth appearance indexes, Mez bioaccumulation, and hypothalamus-pituitary-thyroid (HPT) axis related hormone contents and gene expression after 14 and 28 days exposure. Compared with two cis-Mez, rac-Mez was preferentially bioaccumulated in tadpoles, and rac-Mez treatment showed a higher toxicity effect on tadpole including growth stage and body weight inhibition by dysregulating tadpole thyroid stimulating hormone (TSH) and thyroid hormone (TH) contents and related gene expression. Enantioselectivity was observed in two cis-Mez treatments. Compared with R,S-Mez, S,R-Mez treatment showed more severe damage on tadpole HPT axis related physiological and biochemical processes. rGo could effectively decrease the toxicity of Mez, especially shown the capacity of repairing the hormone dysregulation caused by R,S-Mez treatment. Moreover, the addition of rGo can decrease the bioaccumulation of Mez in tadpoles. Therefore, R,S-Mez is less toxic to Xenopus Laevis larva growth, and its toxicity could be effectively repaired by the addition of rGO.

Denitrification and N2O Emission in Estuarine Sediments in Response to Ocean Acidification: From Process to Mechanism.

Global estuarine ecosystems are experiencing severe nitrogen pollution and ocean acidification (OA) simultaneously. Sedimentary denitrification is an important way of reactive nitrogen removal but at the same time leads to the emission of large amounts of nitrous oxide (N2O), a potent greenhouse gas. It is known that OA in estuarine regions could impact denitrification and N2O production; however, the underlying mechanism is still underexplored. Here, sediment incubation and pure culture experiments were conducted to explore the OA impacts on microbial denitrification and the associated N2O emissions in estuarine sediments. Under neutral (in situ) conditions, fungal N2O emission dominated in the sediment, while the bacterial and fungal sources had a similar role under acidification. This indicated that acidification decreased the sedimentary fungal denitrification and likely inhibited the activity of fungal denitrifiers. To explore molecular mechanisms, a denitrifying fungal strain of Penicillium janthinellum was isolated from the sediments. By using deuterium-labeled single-cell Raman spectroscopy and isobaric tags for relative and absolute quantitation proteomics, we found that acidification inhibited electron transfers in P. janthinellum and downregulated expressions of the proteins related to energy production and conservation. Two collaborative pathways of energy generation in the P. janthinellum were further revealed, that is, aerobic oxidative phosphorylation and TCA cycle and anoxic pyruvate fermentation. This indicated a distinct energy supply strategy from bacterial denitrification. Our study provides insights into fungi-mediated nitrogen cycle in acidifying aquatic ecosystems.

Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables.

Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1-2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and blaTEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.

Profiling the antibiotic resistome in soils between pristine and human-affected sites on the Tibetan Plateau.

With increasing pressure from anthropogenic activity in pristine environments, the comprehensive profiling of antibiotic resistance genes (ARGs) is essential to evaluate the potential risks from human-induced antibiotic resistance in these under-studied places. Here, we characterized the microbial resistome in relatively pristine soil samples collected from four distinct habitats on the Tibetan Plateau, using a Smart chip based high-throughput qPCR approach. We compared these to soils from the same habitats that had been subjected to various anthropogenic activities, including residential sewage discharge, animal farming, atmospheric deposition, and tourism activity. Compared to pristine samples, an average of 23.7% more ARGs were detected in the human-affected soils, and the ARGs enriched in these soils mainly encoded resistances to aminoglycoside and beta-lactam. Of the four habitats studied, soils subjected to animal farming showed the highest risks of ARG enrichment and dissemination. As shown, the number of ARGs enriched (a total of 42), their fold changes (17.6 fold on average), and the co-occurrence complexity between ARGs and mobile genetic elements were all the highest in fecal-polluted soils. As well as antibiotics themselves, heavy metals also influenced ARG distributional patterns in Tibetan environments. However, compared to urban areas, the Tibetan Plateau had a low potential for ARG selection and exhibited low carriage of ARGs by mobile genetic elements, even in environments impacted by humans, suggesting that these ARGs have a limited capacity to disseminate. The present study examined the effects of multiple anthropogenic activities on the soil resistomes in relatively pristine environments.

Stimulation of N2 O emission via bacterial denitrification driven by acidification in estuarine sediments.

Ocean acidification in nitrogen-enriched estuaries has raised global concerns. For decades, biotic and abiotic denitrification in estuarine sediments has been regarded as the major ways to remove reactive nitrogen, but they occur at the expense of releasing greenhouse gas nitrous oxide (N2 O). However, how these pathways respond to acidification remains poorly understood. Here we performed a N2 O isotopocules analysis coupled with respiration inhibition and molecular approaches to investigate the impacts of acidification on bacterial, fungal, and chemo-denitrification, as well as N2 O emission, in estuarine sediments through a series of anoxic incubations. Results showed that acidification stimulated N2 O release from sediments, which was mainly mediated by the activity of bacterial denitrifiers, whereas in neutral environments, N2 O production was dominated by fungi. We also found that the contribution of chemo-denitrification to N2 O production cannot be ignored, but was not significantly affected by acidification. The mechanistic investigation further demonstrated that acidification changed the keystone taxa of sedimentary denitrifiers from N2 O-reducing to N2 O-producing ones and reduced microbial electron-transfer efficiency during denitrification. These findings provide novel insights into how acidification stimulates N2 O emission and modulates its pathways in estuarine sediments, and how it may contribute to the acceleration of global climate change in the Anthropocene.

The predictive value of diabetic retinopathy on subsequent diabetic nephropathy in patients with type 2 diabetes: a systematic review and meta-analysis of prospective studies.

This systematic review and meta-analysis aimed to assess the predictive value of diabetic retinopathy (DR) on further diabetic nephropathy (DN) risk in patients with type 2 diabetes (T2D) based on the prospective cohort studies. PubMed, Embase, and the Cochrane Library were systematically searched for eligible prospective cohort studies through March 2020. The predictive value of DR was assessed using sensitivity, specificity, positive likelihood ratio (PLR) and negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the receiver operating characteristic curve (AUC) through the bivariate generalized linear mixed model and the random-effects model. Ten prospective cohort studies recruited 635 patients with T2D. The pooled sensitivity and specificity of DR for predicted DN were noted to be 0.64 (95% CI, 0.54-0.73) and 0.77 (95% CI, 0.60-0.88), respectively. The pooled PLR and NLR of DR for predicted DN were 2.72 (95% CI, 1.42-5.19) and 0.47 (95% CI, 0.33-0.67), respectively. The summary DOR for the relationship between DR and subsequent DN for T2D patients was 5.53 (95% CI, 2.00-15.30), and the AUC of DR for predicted DN was 0.73 (95% CI, 0.69-0.77). This study found significant associations between DR and subsequent DN risk for patients with T2D. Moreover, the predictive value of DR on subsequent DN risk was relatively lower.

Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation*.

There is an urgent need to develop antiviral drugs and alleviate the current COVID-19 pandemic. Herein we report the design and construction of chimeric oligonucleotides comprising a 2'-OMe-modified antisense oligonucleotide and a 5'-phosphorylated 2'-5' poly(A)4 (4A2-5 ) to degrade envelope and spike RNAs of SARS-CoV-2. The oligonucleotide was used for searching and recognizing target viral RNA sequence, and the conjugated 4A2-5 was used for guided RNase L activation to sequence-specifically degrade viral RNAs. Since RNase L can potently cleave single-stranded RNA during innate antiviral response, degradation efficiencies with these chimeras were twice as much as those with only antisense oligonucleotides for both SARS-CoV-2 RNA targets. In pseudovirus infection models, chimera-S4 achieved potent and broad-spectrum inhibition of SARS-CoV-2 and its N501Y and/or ΔH69/ΔV70 mutants, indicating a promising antiviral agent based on the nucleic acid-hydrolysis targeting chimera (NATAC) strategy.

Optical Control of a CRISPR/Cas9 System for Gene Editing by Using Photolabile crRNA.

Currently CRISPR/Cas9 is a widely used efficient tool for gene editing. Precise control over the CRISPR/Cas9 system with high temporal and spatial resolution is essential for studying gene regulation and editing. Here, we synthesized a novel light-controlled crRNA by coupling vitamin E and a photolabile linker at the 5' terminus to inactivate the CRISPR/Cas9 system. The vitamin E modification did not affect ribonucleoprotein (RNP) formation of Cas9/crRNA/tracrRNA complexes but did inhibit the association of RNP with the target DNA. Upon light irradiation, vitamin E-caged crRNA was successfully activated to achieve light-induced genome editing of vascular endothelial cell-growth factor A (VEGFA) in human cells through a T7E1 assay and Sanger sequencing as well as gene knockdown of EGFP expression in EGFP stably expressing cells. This new caging strategy for crRNA could provide new methods for spatiotemporal photoregulation of CRISPR/Cas9-mediated gene editing.

Developing Novel G-Quadruplex Ligands: from Interaction with Nucleic Acids to Interfering with Nucleic Acid⁻Protein Interaction.

G-quadruplex is a special secondary structure of nucleic acids in guanine-rich sequences of genome. G-quadruplexes have been proved to be involved in the regulation of replication, DNA damage repair, and transcription and translation of oncogenes or other cancer-related genes. Therefore, targeting G-quadruplexes has become a novel promising anti-tumor strategy. Different kinds of small molecules targeting the G-quadruplexes have been designed, synthesized, and identified as potential anti-tumor agents, including molecules directly bind to the G-quadruplex and molecules interfering with the binding between the G-quadruplex structures and related binding proteins. This review will explore the feasibility of G-quadruplex ligands acting as anti-tumor drugs, from basis to application. Meanwhile, since helicase is the most well-defined G-quadruplex-related protein, the most extensive research on the relationship between helicase and G-quadruplexes, and its meaning in drug design, is emphasized.

Thermal Structure-Induced Biochemical Parameters Stratification in a Subtropical Dam Reservoir.

Although stratification in deep lakes is well-discussed, few studies pay attention to thermal structure as well as its influences on stratification of biochemical parameters in subtropical lakes in mountainous cities. Here, we studied the depth profile of temperature and biochemical parameters in Longjing Lake, a subtropical reservoir in a mountainous city. Thermal stratification became strong during summer. Biochemical parameters were strongly associated with thermal structure. Stratification started at 2~6 m depth with a substantial decrease in dissolved oxygen, biochemical oxygen demand (BOD5), chlorophyll a, and pH, corresponding to an increase in total nitrogen, ammonium (), nitrite (), total inorganic nitrogen (TIN), total phosphorus, and soluble reactive phosphorus (SRP) with depth; the majority of biochemical parameters showed slight variations from 12 m downward. Our results indicated the stratification of Longjing Lake was stronger and more stable than the stratification of tropical and temperate lakes in lowland cities.

Transcriptome-wide mapping of small-molecule RNA-binding sites in live cells.

Small molecules targeting RNA can be valuable chemical probes and potential therapeutics. The interactions between small molecules, particularly fragments, and RNA, however, can be difficult to detect due to their modest affinities and short residence times. Here, we describe the procedures for mapping the molecular fingerprints of small molecules in vitro and throughout the human transcriptome in live cells, identifying both the targets bound by the small molecule and the sites of binding therein. For complete details on the use and execution of this protocol, please refer to 1.

Reducing carbon and nitrogen loss by shortening the composting duration based on seed germination index (SCD@GI): Feasibilities and challenges.

Addressing carbon (C) and nitrogen (N) losses through composting has emerged as a critical environmental challenge recently, and how to mitigate these losses has been a hot topic across the world. As the emissions of carbonaceous and nitrogenous gases were closely correlated with the composting process, the feasibility of composting duration shortening on C and N loss needs to be explored. Therefore, the goal of this paper is to find evidence-based approaches to reduce composting duration, utilizing the seed germination index as a metric (SCD@GI), for assessing its efficiency on C and N loss reductions as well as compost quality. Our findings reveal that the terminal seed germination index (GI) frequently surpassed the necessary benchmarks, with a significant portion of trials achieving the necessary GI within 60 % of the standard duration. Notably, an SCD@GI of 80 % resulted in a reduction of CO2 and NH3 by 21.4 % and 21.9 %, respectively, surpassing the effectiveness of the majority of current mitigation strategies. Furthermore, compost quality, maturity specifically, remained substantially unaffected at a GI of 80 %, with the composting process maintaining adequate thermophilic conditions to ensure hygienic quality and maturity. This study also highlighted the need for further studies, including the establishment of uniform GI testing standards and comprehensive life cycle analyses for integrated composting and land application practices. The insights gained from this study would offer new avenues for enhancing C and N retention during composting, contributing to the advancement of high-quality compost production within the framework of sustainable agriculture.

Effects of microplastics on N2O production and reduction potential in crop soils of northern China.

Microplastics (MPs) pollution are found to be increasing in vegetable soils and potentially affecting N2O production and their associated pathways; however, its specific effects remain unclear. Here, we selected two common MPs, PE and PP at four different concentration levels of 0, 0.5, 1.5 and 3%, and conducted several incubation experiments aiming to explore soil bacterial and fungal N2O production. Results showed that the bacteria were the main contributors for the production of N2O, regardless of the absence or presence of MPs; and its contribution was decreased with increasing concentrations of PE and PP. The nosZ clade I and II genes were positively correlated with N2O reduction rates, indicating a combined regulation on soil N2O reduction. PE significantly inhibited the bacterial nitrification and denitrification, but did not affect the total N2O production rates; while PP significantly reduced both the bacterial and fungal N2O production rates. The resistance of fungal N2O production to MPs pollution was stronger than that of the bacterial N2O production. It highlights that the MPs pollution could reduce the potential of N2O production and reduction, and thus disturb soil nitrogen cycling system; while the inhibition on N2O production via bacteria and fungi varies with different types of MPs. This study is conducive to an improved and more comprehensive understanding of the ecological impacts of MPs within the agroecosystem.

Responses of soil bacterial and fungal denitrification and associated N2O emissions to organochloride pesticide.

The extensive application of organochloride pesticides in agriculture has raised concerns about their potential negative impacts on soil microbial denitrification and associated N2O emissions. However, most studies have primarily focused on bacteria, and the contribution of fungi to N2O emissions and their response to organochloride pesticides have often been overlooked. In this study, 15N tracing combined with the respiration inhibition method was applied to examine the impacts of chlorothalonil on both fungal and bacterial denitrification. The results demonstrated that fungal N2O emissions dominated in the absence of chlorothalonil, accounting for 73 % of total N2O emissions. Chlorothalonil inhibited fungal and bacterial denitrification via different mechanisms and altered the main pathways of soil N2O emissions. Amplicon sequencing analyses indicated that chlorothalonil significantly reduced the abundances of N2O-producing fungi owing to its fungicidal effect and fungal N2O emissions significantly dropped. Molecular biological analyses revealed that chlorothalonil induced lower electron generation, transport, and consumption efficiencies, which led to the inhibition of denitrifying enzymes in bacteria. Bacterial N2O emissions dramatically increased and became the dominant source. These findings provide insights into the mechanisms by which N2O emissions from fungal and bacterial denitrification are influenced by chlorothalonil.

Synthesis of α-Boryl Ketones via Hydration or Oxidation of B(MIDA)-Decorated Alkynes.

α-Boryl ketones are traditionally challenging targets in organic synthesis. Reported herein is a mild and metal-free synthesis of α-boryl ketones via the hydration or oxidation of N-methyliminodiacetyl boronate (B(MIDA))-decorated alkynes. A new hydration system comprised of AcCl and H2O in HFIP allows the hydration of arylethynyl B(MIDA)s at room temperature with decent functional group tolerance. An oxidative carbon deletion process of propargylic B(MIDA)s is also developed for the synthesis of aliphatic α-boryl ketones. An intriguing ß-boron effect was observed to account for the unique site- and chemoselectivities. The application of the products in the synthesis of borylated heterocycles was demonstrated.

Characterization of microbial community, ecological functions and antibiotic resistance in estuarine plastisphere.

The plastisphere is a new ecological niche. Compared to the surrounding water, microbial community composition associated with the plastisphere is known to differ with functional consequences. Here, this study characterized the bacterial and fungal communities associated with four types of plastisphere (polyethylene, polystyrene, polypropylene and polyvinyl chloride) in an estuarine habitat; assessed ecological functions including carbon, nitrogen, phosphorus and sulfur cycling, and determined the presence of antibiotic resistance genes (ARGs) and human pathogens. Stochastic processes dominated the community assembly of microorganisms on the plastisphere. Several functional genera related to nutrient cycling were enriched in the plastisphere. Compared to surrounding water and other plastisphere, the abundances of carbon, nitrogen and phosphorus cycling genes (cdaR, nosZ and chpy etc.) and ARGs (aadA2-1, cfa and catB8 etc.) were significantly increased in polyvinyl chloride plastisphere. In contrast, the polystyrene plastisphere was the preferred substrate for several pathogens being enriched with for example, Giardia lamblia 18S rRNA, Klebsiella pneumoniae phoE and Legionella spp. 23S rRNA. Overall, this study showed that different plastisphere had different effects on ecological functions and health risk in estuaries and emphasizes the importance of controlling plastic pollution in estuaries. Data from this study support global policy drivers that seek to reduce plastic pollution and offer insights into ecological functions in a new ecological niche of the Anthropocene.