Mechanism of flavonols on detoxification, migration and transformation of indium in rhizosphere system.

Soil contamination by toxic heavy metal induces serious environmental hazards. In recent years, the use of indium (In) in semiconductor products has increased considerably and the release of In is inevitable, which will pose great risk to the ecosystem. The interaction between metal and plants which are the fundamental components of all ecosystems are an indispensable aspect of indium assessment and remediation. The role of flavonols, which is essential to plant resistance to In stress, remains largely unknown. FLS1 related lines of A. thaliana (Col, fls1-3 and OE) were exposed to In stress in soil and flavonols as root exudates were analyzed in exogenous application test. The accumulation and release of flavonols could be induced by In stress. However, flavonols exhibited different function in vivo and in vitro of plant. The basic function of flavonols was to affect root morphology via regulating auxin, but being intervened by In stress. The synthesis and accumulation of flavonols in vivo could activate the antioxidant system and the metal detoxification system to alleviate the toxic effects of In on plant. In addition, plants could make phone calls to rhizosphere microbes for help when exposed to In. Flavonols in vitro might act as the information transmission. Combination of endogenous and exogenous flavonols could affect the migration and transformation of In in soil-plant system via metal complexation and transportation pathway.

Continuous and low-carbon production of biomass flash graphene.

Flash Joule heating (FJH) is an emerging and profitable technology for converting inexhaustible biomass into flash graphene (FG). However, it is challenging to produce biomass FG continuously due to the lack of an integrated device. Furthermore, the high-carbon footprint induced by both excessive energy allocation for massive pyrolytic volatiles release and carbon black utilization in alternating current-FJH (AC-FJH) reaction exacerbates this challenge. Here, we create an integrated automatic system with energy requirement-oriented allocation to achieve continuous biomass FG production with a much lower carbon footprint. The programmable logic controller flexibly coordinated the FJH modular components to realize the turnover of biomass FG production. Furthermore, we propose pyrolysis-FJH nexus to achieve biomass FG production. Initially, we utilize pyrolysis to release biomass pyrolytic volatiles, and subsequently carry out the FJH reaction to focus on optimizing the FG structure. Importantly, biochar with appropriate resistance is self-sufficient to initiate the FJH reaction. Accordingly, the medium-temperature biochar-based FG production without carbon black utilization exhibited low carbon emission (1.9 g CO2-eq g-1 graphene), equivalent to a reduction of up to ~86.1% compared to biomass-based FG production. Undoubtedly, this integrated automatic system assisted by pyrolysis-FJH nexus can facilitate biomass FG into a broad spectrum of applications.

Mitigating Contaminant-Driven Risks for the Safe Expansion of the Agricultural-Sanitation Circular Economy in an Urbanizing World.

The widespread adoption of an agricultural circular economy requires the recovery of resources such as water, organic matter, and nutrients from livestock manure and sanitation. While this approach offers many benefits, we argue this is not without potential risks to human and environmental health that largely stem from the presence of contaminants in the recycled resources (e.g., pharmaceuticals, pathogens). We discuss context specific challenges and solutions across the three themes: (1) contaminant monitoring; (2) collection transport and treatment; and (3) regulation and policy. We advocate for the redesign of sanitary and agricultural management practices to enable safe resource reuse in a proportionate and effective way. In populous urban regions with access to sanitation provision, processes can be optimized using emergent technologies to maximize removal of contaminant from excreta prior to reuse. Comparatively, in regions with limited existing capacity for conveyance of excreta to centralized treatment facilities, we suggest efforts should focus on creation of collection facilities (e.g., pit latrines) and decentralized treatment options such as composting systems. Overall, circular economy approaches to sanitation and resource management offer a potential solution to a pressing challenge; however, to ensure this is done in a safe manner, contaminant risks must be mitigated.

Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities.

The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.

Biological Interactions Mediate Soil Functions by Altering Rare Microbial Communities.

Soil microbes, the main driving force of terrestrial biogeochemical cycles, facilitate soil organic matter turnover. However, the influence of the soil fauna on microbial communities remains poorly understood. We investigated soil microbiota dynamics by introducing competition and predation among fauna into two soil ecosystems with different fertilization histories. The interactions significantly affected rare microbial communities including bacteria and fungi. Predation enhanced the abundance of C/N cycle-related genes. Rare microbial communities are important drivers of soil functional gene enrichment. Key rare microbial taxa, including SM1A02, Gammaproteobacteria, and HSB_OF53-F07, were identified. Metabolomics analysis suggested that increased functional gene abundance may be due to specific microbial metabolic activity mediated by soil fauna interactions. Predation had a stronger effect on rare microbes, functional genes, and microbial metabolism compared to competition. Long-term organic fertilizer application increased the soil resistance to animal interactions. These findings provide a comprehensive understanding of microbial community dynamics under soil biological interactions, emphasizing the roles of competition and predation among soil fauna in terrestrial ecosystems.

Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development.

Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.

Interaction of tetracycline and copper co-intake in inducing antibiotic resistance genes and potential pathogens in mouse gut.

The widespread use of copper and tetracycline as growth promoters in the breeding industry poses a potential threat to environmental health. Nevertheless, to the best of our knowledge, the potential adverse effects of copper and tetracycline on the gut microbiota remain unknown. Herein, mice were fed different concentrations of copper and/or tetracycline for 6 weeks to simulate real life-like exposure in the breeding industry. Following the exposure, antibiotic resistance genes (ARGs), potential pathogens, and other pathogenic factors were analyzed in mouse feces. The co-exposure of copper with tetracycline significantly increased the abundance of ARGs and enriched more potential pathogens in the gut of the co-treated mice. Copper and/or tetracycline exposure increased the abundance of bacteria carrying either ARGs, metal resistance genes, or virulence factors, contributing to the widespread dissemination of potentially harmful genes posing a severe risk to public health. Our study provides insights into the effects of copper and tetracycline exposure on the gut resistome and potential pathogens, and our findings can help reduce the risks associated with antibiotic resistance under the One Health framework.

Sustainable Blue Foods from Rice-Animal Coculture Systems.

Global interest grows in blue foods as part of sustainable diets, but little is known about the potential and environmental performance of blue foods from rice-animal coculture systems. Here, we compiled a large experimental database and conducted a comprehensive life cycle assessment to estimate the impacts of scaling up rice-fish and rice-crayfish systems in China. We find that a large amount of protein can be produced from the coculture systems, equivalent to ∼20% of freshwater aquaculture and ∼70% of marine wild capture projected in 2030. Because of the ecological benefits created by the symbiotic relationships, cocultured fish and crayfish are estimated to be carbon-negative (-9.8 and -4.7 kg of CO2e per 100 g of protein, respectively). When promoted at scale to displace red meat, they can save up to ∼98 million tons of greenhouse gases and up to ∼13 million hectares of farmland, equivalent to ∼44% of China's total rice acreage. These results suggest that rice-animal coculture systems can be an important source of blue foods and contribute to a sustainable dietary shift, while reducing the environmental footprints of rice production. To harvest these benefits, robust policy supports are required to guide the sustainable development of coculture systems and promote healthy and sustainable dietary change.

Managing fragmented croplands for environmental and economic benefits in China.

Cropland fragmentation contributes to low productivity and high abandonment risk. Using spatial statistics on a detailed land use map, we show that 10% of Chinese croplands have no potential to be consolidated for large-scale farming (>10 ha) owing to spatial constraints. These fragmented croplands contribute only 8% of total crop production while using 15% of nitrogen fertilizers, leading to 12% of fertilizer loss in China. Optimizing the cropping structure of fragmented croplands to meet animal food demand in China can increase animal food supply by 19%, equivalent to increasing cropland proportionally. This crop-switching approach would lead to a 10% and 101% reduction in nitrogen and greenhouse gas emissions, respectively, resulting in a net benefit of US$ 7 billion yr-1. If these fragmented croplands were relocated to generate large-scale farming units, livestock, vegetable and fruit production would be increased by 8%, 3% and 14%, respectively, and reactive nitrogen and greenhouse gas emissions would be reduced by 16% and 5%, respectively, resulting in a net benefit of US$ 44 billion yr-1. Both solutions could be used to achieve synergies between food security, economic benefits and environmental protection through increased agricultural productivity, without expanding the overall cropland area.

Canopy nitrogen deposition enhances soil ecosystem multifunctionality in a temperate forest.

Nitrogen (N) deposition affects ecosystem functions crucial to human health and well-being. However, the consequences of this scenario for soil ecosystem multifunctionality (SMF) in forests are poorly understood. Here, we conducted a long-term field experiment in a temperate forest in China, where N deposition was simulated by adding N above and under the canopies. We discover that canopy N addition promotes SMF expression, whereas understory N addition suppresses it. SMF was regulated by fungal diversity in canopy N addition treatments, which is largely due to the strong resistance to soil acidification and efficient resource utilization characteristics of fungi. While in understory N addition treatments, SMF is regulated by bacterial diversity, which is mainly because of the strong resilience to disturbances and fast turnover of bacteria. Furthermore, rare microbial taxa may play a more important role in the maintenance of the SMF. This study provides the first evidence that N deposition enhanced SMF in temperate forests and enriches the knowledge on enhanced N deposition affecting forest ecosystems. Given the divergent results from two N addition approaches, an innovative perspective of canopy N addition on soil microbial diversity-multifunctionality relationships is crucial to policy-making for the conservation of soil microbial diversity and sustainable ecosystem management under enhanced N deposition. In future research, the consideration of canopy N processes is essential for more realistic assessments of the effects of atmospheric N deposition in forests.

Biogeographic patterns and drivers of soil viromes.

Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.

A database on the abundance of environmental antibiotic resistance genes.

Antimicrobial resistance (AMR) poses a severe threat to global health. The wide distribution of environmental antibiotic resistance genes (ARGs), which can be transferred between microbiota, especially clinical pathogens and human commensals, contributed significantly to AMR. However, few databases on the spatiotemporal distribution, abundance, and health risk of ARGs from multiple environments have been developed, especially on the absolute level. In this study, we compiled the ARG occurrence data generated by a high-throughput quantitative PCR platform from 1,403 samples in 653 sampling sites across 18 provinces in China. The database possessed 291,870 records from five types of habitats on the abundance of 290 ARGs, as well as 8,057 records on the abundance of 30 mobile genetic elements (MGEs) from 2013 to 2020. These ARGs conferred resistance to major common types of antibiotics (a total of 15 types) and represented five major resistance mechanisms, as well as four risk ranks. The database can provide information for studies on the dynamics of ARGs and is useful for the health risk assessment of AMR.

Effects of common artificial sweeteners at environmentally relevant concentrations on soil springtails and their gut microbiota.

Artificial sweeteners (AS) are extensively utilized as sugar substitutes and have been recognized as emerging environmental contaminants. While the effect of AS on aquatic organisms has garnered recent attention, their effects on soil invertebrates and gut microbial communities remain unclear. To address this knowledge gap, we exposed springtails (Folsomia candida) to both single and combined treatments of four typical AS (sucralose [SUC], saccharin [SAC], cyclamate [CYC], and acesulfame [ACE]) at environmentally relevant concentrations of 0.01, 0.1 and 1 mg kg-1 in soil. Following the first-generational exposure, the reproduction of juveniles showed a significant increase under all the AS treatments of 0.1 mg kg-1. The transcriptomic analysis revealed significant enrichment of several Kyoto Encyclopedia of Gene and Genome pathways (e.g., glycolysis/gluconeogenesis, pentose and glucuronate interconversions, amino sugar, and nucleotide sugar metabolism, ribosome, and lysosome) in springtails under all AS treatments. Analysis of gut bacterial microbiota indicated that three AS (SUC, CYC, and ACE) significantly decreased alpha diversity, and all AS treatments increased the abundance of the genus Achromobacter. After the sixth-generational exposure to CYC, weight increased, but reproduction was inhibited. The pathways that changed significantly (e.g., extracellular matrix-receptor interaction, amino sugar and nucleotide sugar metabolism, lysosome) were generally similar to those altered in first-generational exposure, but with opposite regulation directions. Furthermore, the effect on the alpha diversity of gut microbiota was contrary to that after first-generational exposure, and more noticeable disturbances in microbiota composition were observed. These findings underscore the ecological risk of AS in soils and improve our understanding of the toxicity effects of AS on living organisms.

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 biogeography and ecological implications of cobamide-producing prokaryotes.

Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 nonredundant metagenome-assembled genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities were observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.

Spatiotemporal Changes of Antibiotic Resistance, Potential Pathogens, and Health Risk in Kindergarten Dust.

The microorganisms present in kindergartens are extremely important for children's health during their three-year preschool education. To assess the risk of outdoor dust in kindergartens, the antibiotic resistome and potential pathogens were investigated in dust samples collected from 59 kindergartens in Xiamen, southeast China in both the winter and summer. Both high-throughput quantitative PCR and metagenome analysis revealed a higher richness and abundance of antibiotic resistance genes (ARGs) in winter (P < 0.05). Besides, the bloom of ARGs and potential pathogens was evident in the urban kindergartens. The co-occurrence patterns among ARGs, mobile genetic elements (MGEs), and potential pathogens suggested some bacterial pathogens were potential hosts of ARGs and MGEs. We found a large number of high-risk ARGs in the dust; the richness and abundance of high-risk ARGs were higher in winter and urban kindergartens compared to in summer and peri-urban kindergartens, respectively. The results of the co-occurrence patterns and high-risk ARGs jointly reveal that urbanization will significantly increase the threat of urban dust to human beings and their risks will be higher in winter. This study unveils the close association between ARGs/mobile ARGs and potential pathogens and emphasizes that we should pay more attention to the health risks induced by their combination.

Divergent Fate and Roles of Dissolved Organic Matter from Spatially Varied Grassland Soils in China During Long-Term Biogeochemical Processes.

Terrestrial dissolved organic matter (DOM) is critical to global carbon and nutrient cycling, climate change, and human health. However, how the spatial and compositional differences of soil DOM affect its dynamics and fate in water during the carbon cycle is largely unclear. Herein, the biodegradation of DOM from 14 spatially distributed grassland soils in China with diverse organic composition was investigated by 165 days of incubation experiments. The results showed that although the high humified fraction (high-HS) regions were featured by high humic-like fractions of 4-25 kDa molecular weight, especially the abundant condensed aromatics and tannins, they unexpectedly displayed greater DOM degradation during 45-165 days. In contrast, the unique proteinaceous and 25-100 kDa fractions enriched in the low humified fraction (low-HS) regions were drastically depleted and improved the decay of bulk DOM but only during 0-45 days. Together, DOM from the high-HS regions would cause lower CO2 outgassing to the atmosphere but higher organic loads for drinking water production in the short term than that from the low-HS regions. However, this would be reversed for the two regions during the long-term transformation processes. These findings highlight the importance of spatial and temporal variability of DOM biogeochemistry to mitigate the negative impacts of grassland soil DOM on climate, waters, and humans.

Aboveground plants determine the exchange of pathogens within air-phyllosphere-soil continuum in urban greenspaces.

The microbiome in the air-phyllosphere-soil continuum of urban greenspaces plays a crucial role in re-connecting urban populations with biodiverse environmental microbiomes. However, little is known about whether plant type affects the airborne microbiomes, as well as the extent to which soil and phyllosphere microbiomes contribute to airborne microbiomes. Here we collected soil, phyllosphere and airborne microbes with different plant types (broadleaf tree, conifer tree, and grass) in urban parks. Despite the significant impacts of plant type on soil and phyllosphere microbiomes, plant type had no obvious effects on the diversity of airborne microbes but shaped airborne bacterial composition in urban greenspaces. Soil and phyllosphere microbiomes had a higher contribution to airborne bacteria in broadleaf trees (37.56%) compared to conifer trees (9.51%) and grasses (14.29%). Grass areas in urban greenspaces exhibited a greater proportion of potential pathogens compared to the tree areas. The abundance of bacterial pathogens in phyllosphere was significantly higher in grasses compared to broadleaf and conifer trees. Together, our study provides novel insights into the microbiome patterns in air-phyllosphere-soil continuum, highlighting the potential significance of reducing the proportion of extensively human-intervened grass areas in future urban environment designs to enhance the provision of ecosystem services in urban greenspaces.

The soil plastisphere.

Understanding the effects of plastic pollution in terrestrial ecosystems is a priority in environmental research. A central aspect of this suite of pollutants is that it entails particles, in addition to chemical compounds, and this makes plastic quite different from the vast majority of chemical environmental pollutants. Particles can be habitats for microbial communities, and plastics can be a source of chemical compounds that are released into the surrounding environment. In the aquatic literature, the term 'plastisphere' has been coined to refer to the microbial community colonizing plastic debris; here, we use a definition that also includes the immediate soil environment of these particles to align the definition with other concepts in soil microbiology. First, we highlight major differences in the plastisphere between aquatic and soil ecosystems, then we review what is currently known about the soil plastisphere, including the members of the microbial community that are enriched, and the possible mechanisms underpinning this selection. Then, we focus on outlining future prospects for research on the soil plastisphere.