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It has been documented that human activities are causing the rapid loss of taxonomic, phylogenetic, genetic and functional diversity in soils. However, it remains unclear how modern intensive rice cultivation impacts the soil microbiome and its functionality. Here we examined the microbial composition and function differences between a buried Neolithic paddy soil and an adjacent, currently-cultivated paddy soil using high throughput metagenomics technologies. Our results showed that the currently cultivated soil contained about 10-fold more microbial biomass than the buried one. Analyses based on both 16S rRNA genes and functional gene array showed that the currently cultivated soil had significantly higher phylogenetic diversity, but less functional diversity than the buried Neolithic one. The community structures were significantly different between modern and ancient soils, with functional structure shifting towards accelerated organic carbon (C) degradation and nitrogen (N) transformation in the modern soils. This study implies that, modern intensive rice cultivation has substantially altered soil microbial functional structure, leading to functional homogenization and the promotion of soil ecological functions related to the acceleration of nutrient cycling which is necessary for high crop yields.

Introduction: To evaluate the efficacy of probiotics in preventing nosocomial pneumonia in critically ill patients.Methods: We searched PubMed, EMBASE, and the Web of Science for relevant studies. Two reviewers extracted data and reviewed the quality of th

It is well established that the presence of soluble amyloid-beta protein (Abeta) correlates with the severity of dementia in Alzheimer's disease (AD). Several lines of evidence indicate that cyclic AMP responsive element binding protein (CREB) and protein kinase A (PKA) are involved in soluble Abeta-trigged disruption of synaptic plasticity in early AD. Previously we demonstrated the beneficial effects of ginsenoside Rg1 on Abeta-induced neuronal insult. Therefore, in the present study, we examined the effects of long-term consumption of Rg1 on the cerebral Abeta content and PKA/CREB signaling molecules, as well as cognitive performance in senescence-accelerated mouse prone 8 (SAMP8). Notably, a significant dose-dependent reduction of soluble Abeta(1-40) was shown in the hippocampus of SAMP8 mice after administration with ginsenoside Rg1 for 3 months. Furthermore, Rg1 treatment resulted in a significant decrease of hippocampal PKA RIIalpha level (isoform IIalpha of the regulatory subunit of PKA). In contrast, phospho-CREB and brain derived neurotrophic factor (BDNF) levels were dramatically increased in the hippocampus of SAMP8 treated with Rg1. Additionally, administration of ginsenoside Rg1 consequently improved learning and memory outcomes in SAMP8 mice. These data suggest that long-term consumption of ginsenoside Rg1 may delay cognitive decline, associated with significant effects on Abeta generation, PKA/CREB activity, as well as BDNF content in the brain. These data provide further support for the therapeutic or intervention potency of ginsenoside Rg1 in the early stage of AD. [ABSTRACT FROM AUTHOR]

Microplastic is globally regarded as an important factor impacting biogeochemical cycles, yet our understanding of such influences is limited by the uncertainties of intricate microbial processes. By multiomics analysis, coupled with soil chemodiversity characterization and microbial carbon use efficiency (CUE), we investigated how microbial responses to microplastics impacted soil carbon cycling in a long-term field experiment. We showed that biodegradable microplastics promoted soil organic carbon accrual by an average of 2.47%, while nondegradable microplastics inhibited it by 17.4%, as a consequence of the virus-bacteria coadaptations to the microplastics disturbance. In the relevant functional pathways, nondegradable microplastics significantly ( P < 0.05) enhanced the abundance and transcriptional activity related to complex carbohydrate metabolism, whereas biodegradable microplastics significantly ( P < 0.05) promoted functions involved in amino acid metabolism and glycolysis. Accordingly, viral lysis enhanced in nondegradable microplastics treatments to introduce more complex organic compounds to soil dissolved organic matters, thus benefiting the oligotrophs with high carbon metabolic capabilities in exploitation competition. In contrast, biodegradable microplastics enriched viral auxiliary metabolic genes of carbon metabolism through "piggyback-the-winner" strategy, conferring to dominant copiotrophs, enhanced substrate utilization capabilities. These virus-host interactions were also demonstrated in the corresponding soil plastisphere, which would alter microbial resource allocation and metabolism via CUE, affecting carbon storage consequently. Overall, our results underscore the importance of viral-host interactions in understanding the microplastics-dependent carbon storage in the soil ecosystem., Competing Interests: Competing interests statement:The authors declare no competing interest.

Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Antibiotic resistance is currently an unfolding global crisis threatening human health worldwide. While antibiotic resistance genes (ARGs) are known to be pervasive in environmental media, the occurrence of antibiotic resistance at interfaces between two or more adjacent media is largely unknown. Here, we designed a microcosm study to simulate plastic pollution in paddy soil and used a novel method, stimulated Raman scattering coupled with deuterium oxide (D 2 O) labelling, to compare the antibiotic resistance in a single medium with that at the interface of multiple environmental media (plastic, soil, water). Results revealed that the involvement of more types of environmental media at interfaces led to a higher proportion of active resistant bacteria. Genotypic analysis showed that ARGs (especially high-risk ARGs) and mobile genetic elements (MGEs) were all highly enriched at the interfaces. This enrichment was further enhanced by the co-stress of heavy metal (arsenic) and antibiotic (ciprofloxacin). Our study is the first to apply stimulated Raman scattering to elucidate antibiotic resistance at environmental interfaces and reveals novel pathway of antibiotic resistance dissemination in the environment and overlooked risks to human health., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

While substantial amounts of antibiotics and pesticides are applied to maintain orchard yields, their influence on the dissemination and risk of antibiotic resisitome in the orchard food chain remains poorly understood. In this study, we characterized the bacterial and fungal communities and differentiated both antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the soil, Chinese bayberry (matured and fallen), and fruit fly gut, collected from five geographic locations. Our results showed that fruit fly guts and soils exhibit a higher abundance of ARGs and VFGs compared with bayberry fruits. We identified 112 shared ARGs and 75 shared VFGs, with aminoglycoside and adherence factor genes being among the most abundant. The co-occurrence network revealed some shared microbes, such as Bacillus and Candida , as potential hosts of ARGs, highlighting the vector risks for both above- and below-ground parts of the orchard food chain. Notably, the elevated levels of antibiotics and pesticide residues in orchard soils increase ARGs, mobile genetic elements (MGEs), and VFGs in the soil-bayberry-fruit fly food chain. Our study highlighted that agricultural management, including the overuse of antibiotics and pesticides, could be the key factor in accumulating resistomes in the orchard food chain.

Active antibiotic-resistant bacteria (ARB) play a major role in spreading antimicrobial resistance (AMR) in the environment; however, they have remained largely unexplored. Herein, we coupled bio-orthogonal noncanonical amino acid tagging with high-throughput fluorescence-activated single-cell sorting (FACS) and sequencing to characterize the phenome and genome of active ARB in complex environmental matrices. Active ARB, conferring resistance to six antibiotics throughout wastewater treatment, were distinguished and quantified. The percentage and concentration of active ARB ranged from 0.28% to 45.3% and from 1.1 × 10 4 to 2.09 × 10 7 cells/mL, respectively. Notably, the final effluents retained up to 4.79 × 10 4 cells/mL of active ARB. Targeted FACS and genomic sequencing revealed a distinct taxonomic composition of active ARB compared with that of the overall population. The coexistence of antibiotic resistome and mobilome in active ARB was also identified, including three high-quality metagenomic assembly genomes assigned to pathogenic bacteria, highlighting the substantial health risks due to their activity, phenotypic resistance, mobility, and pathogenicity. This study advances our understanding of previously overlooked active ARB in the environment by linking their resistance phenotype to their genotype. This high-throughput method will enable efficient quantitative surveillance of active AMR, providing valuable insights into risk control and management.

High arsenic (As), fluoride (F - ), and microbial pathogens coexist in semiarid conditions afflicting > 240 million people worldwide including Pakistan. Groundwater quality has declined due to geogenic and manmade activities providing suitable ground for ubiquity, bioavailability, and toxicity of contaminants. We tested the health hazard, distribution, and apportionment of As, F - , and microbes in groundwater around coal mines in Quetta, Pakistan. The range of As, and F - concentrations in groundwater were 0.2-16.6 µg/L, 0.4-18.5 mg/L. Both, As and F - correlate with high HCO 3 - , pH, Na + , SO 4 2- , Fe , and Mn, and negatively with Ca 2+ water. The coalfield showed many folds higher As 15.8-28.5 µg/L, and F - 10.8-34.5 mg/L compared to groundwater-wells. Geochemical phases revealed saturation of groundwater with calcite, dolomite, fluorite, gypsum, and undersaturation with halite-mirabilite, and arsenopyrite minerals. The positive matrix factorization (PMF) model assessed five-factor solutions: geogenic, industrial, coal mining, sulfide & fluoride-bearing mineral-dissolution, and agriculture pollution delivered As, F - , and microbial contamination. About 24.6 % and 64.4 % of groundwater samples exceeded the WHO guidelines of As 10 µg/L, F - 1.5 mg/L. The carcinogenicity, and non-carcinogenicity of As, and F - were higher in children than adults. Therefore, health hazards in children are of great concern in achieving sustainable management goals., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Nitrous oxide (N 2 O) is a potent greenhouse gas with various production pathways. N 2 O reductase (N 2 OR) is the primary N 2 O sink, but the distribution of its gene clades, typically nosZ I and atypically nosZ II, along urbanization gradients remains poorly understood. Here we sampled soils from forests, parks, and farmland across eight provinces in eastern China, using high-throughput sequencing to distinguish between two N 2 O-reducing bacteria clades. A deterministic process mainly determined assemblies of the nosZ I communities. Homogeneous selection drove nosZ I deterministic processes, and both homogeneous and heterogeneous selection influenced nosZ II. This suggests nosZ II is more sensitive to environmental changes than nosZ I, with significant changes in community structure over time or space. Ecosystems with stronger anthropogenic disturbance, such as urban areas, provide diverse ecological niches for N 2 O-reducing bacteria (especially nosZ II) to adapt to environmental fluctuations. Structural equation modeling (SEM) and correlation analyses revealed that pH significantly influences the community composition of both N 2 O-reducing bacteria clades. This study underscores urbanization's impact on N 2 O-reducing bacteria in urban soils, highlighting the importance of nosZ II and survival strategies. It offers novel insights into the role of atypical denitrifiers among N 2 O-reducing bacteria, underscoring their potential ecological importance in mitigating N 2 O emissions from urban soils.

The spread of antibiotic resistance genes (ARGs) poses a substantial threat to human health. Phage-mediated transduction could exacerbate ARG transmission. While several case studies exist, it is yet unclear to what extent phages encode and mobilize ARGs at the global scale and whether human impacts play a role in this across different habitats. Here, we combine 38,605 bacterial genomes, 1432 metagenomes, and 1186 metatranscriptomes across 12 contrasting habitats to explore the distribution of prophages and their cargo ARGs in natural and human-impacted environments. Worldwide, we observe a significant increase in the abundance, diversity, and activity of prophage-encoded ARGs in human-impacted habitats linked with relatively higher risk of past antibiotic exposure. This effect was driven by phage-encoded cargo ARGs that could be mobilized to provide increased resistance in heterologous E. coli host for a subset of analyzed strains. Our findings suggest that human activities have altered bacteria-phage interactions, enriching ARGs in prophages and making ARGs more mobile across habitats globally., (© 2024. The Author(s).)

This study investigates the spatial and temporal dynamics of air quality in Shandong Province from 2016 to 2022. The Air Quality Index (AQI) showed a seasonal pattern, with higher values in winter due to temperature inversions and heating emissions, and lower values in summer aided by favorable dispersion conditions. The AQI improved significantly, decreasing by approximately 39.4 % from 6.44 to 3.90. Coastal cities exhibited better air quality than inland areas, influenced by industrial activities and geographical features. For instance, Zibo's geography restricts pollutant dispersion, resulting in poor air quality. CO levels remained stable, while O 3 increased seasonally due to photochemical reactions in summer, with correlation coefficients indicating a strong positive correlation with temperature (r = 0.65). Winter saw elevated NO 2 levels linked to heating and vehicular emissions, with an observed increase in correlation with AQI (r = 0.78). PM 2.5 and PM 10 concentrations were higher in colder months due to heating and atmospheric dust, showing a significant decrease of 45 % and 40 %, respectively, over the study period. Predictive modeling forecasts continued air quality improvements, contingent on sustained policy enforcement and technological advancements. This approach provides a comprehensive framework for future air quality management and improvement., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Agriculture's global environmental impacts are widely expected to continue expanding, driven by population and economic growth and dietary changes. This Review highlights climate change as an additional amplifier of agriculture's environmental impacts, by reducing agricultural productivity, reducing the efficacy of agrochemicals, increasing soil erosion, accelerating the growth and expanding the range of crop diseases and pests, and increasing land clearing. We identify multiple pathways through which climate change intensifies agricultural greenhouse gas emissions, creating a potentially powerful climate change-reinforcing feedback loop. The challenges raised by climate change underscore the urgent need to transition to sustainable, climate-resilient agricultural systems. This requires investments that both accelerate adoption of proven solutions that provide multiple benefits, and that discover and scale new beneficial processes and food products.

Earthworms can redistribute soil microbiota, and thus might affect the profile of virulence factor genes (VFGs) which are carried by pathogens in soils. Nevertheless, the knowledge of VFG profile in the earthworm guts and its interaction with earthworm gut microbiome is still lacking. Herein, we characterized earthworm gut and soil microbiome and VFG profiles in natural and agricultural ecosystems at a national scale using metagenomics. VFG profiles in the earthworm guts significantly differed from those in the surrounding soils, which was mainly driven by variations of bacterial communities. Furthermore, the total abundance of different types of VFGs in the earthworm guts was about 20-fold lower than that in the soils due to the dramatic decline (also by approximately 20-fold) of VFG-carrying bacterial pathogens in the earthworm guts. Additionally, five VFGs related to nutritional/metabolic factors and stress survival were identified as keystones merely in the microbe-VFG network in the earthworm guts, implying their pivotal roles in facilitating pathogen colonization in earthworm gut microhabitats. These findings suggest the potential roles of earthworms in reducing risks related to the presence of VFGs in soils, providing novel insights into earthworm-based bioremediation of VFG contamination in terrestrial ecosystems., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Dibromoethane is a widespread, persistent organic pollutant. Biochars are known mediators of reductive dehalogenation by layered Fe II -Fe III hydroxides (green rust), which can reduce 1,2-dibromoethane to innocuous bromide and ethylene. However, the critical characteristics that determine mediator functionality are lesser known. Fifteen biochar substrates were pyrolyzed at 600 °C and 800 °C, characterized by elemental analysis, X-ray photo spectrometry C and N surface speciation, X-ray powder diffraction, specific surface area analysis, and tested for mediation of reductive debromination of 1,2-dibromoethane by a green rust reductant under anoxic conditions. A statistical analysis was performed to determine the biochar properties, critical for debromination kinetics and total debromination extent. It was shown that selected plant based biochars can mediate debromination of 1,2-dibromoethane, that the highest first order rate constant was 0.082/hr, and the highest debromination extent was 27% in reactivity experiments with 0.1 µmol (20 µmol/L) 1,2-dibromoethane, ≈ 22 mmol/L Fe II GR , and 0.12 g/L soybean meal biochar (7 days). Contents of Ni, Zn, N, and P, and the relative contribution of quinone surface functional groups were significantly (p < 0.05) positively correlated with 1,2-dibromoethane debromination, while adsorption, specific surface area, and the relative contribution of pyridinic N oxide surface groups were significantly negatively correlated with debromination., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Conventional bulk molecular approaches, often limited by their destructive nature and low spatial resolution, face challenges when probing the intricate dynamics of the plastisphere. Here, we outline a framework employing Raman spectroscopy combined with stable isotope profiling (SIP) to interrogate the physiological function of the plastisphere microbiome and track its evolutionary trajectories., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Metals/metalloids, being ubiquitous in the environment, can function as a co-selective pressure on antibiotic resistance genes (ARGs) threatening human health. However, the effect of geogenic arsenic (As) on groundwater antibiotic resistomes and their health risks remain largely unknown. Here, we systematically analyzed bacterial communities, pathogenic bacteria, antibiotic resistomes, and in-situ multidrug-resistant isolates with the assessment of the health risk of ARGs and the pathogenicity of their hosts in high As groundwater from the Hetao basin, Northwestern China. We found that long-term geogenic As exposure shifted the assembly of resistomes and resulted in a high abundance and diversity of ARGs in groundwater. Significantly positive associations among As, As cycling genes, ARGs, and mobile genetic elements (MGEs) revealed by network and pathway analyses, together with genetic evidence of As-tolerant multidrug-resistant isolates by whole genomic sequencing, robustly indicate the geogenic As-induced co-selection for antibiotic resistance in groundwater. Variance partitioning analysis further confirmed the determinative role of geogenic As in groundwater resistomes, with As species and As cycling genes as the core abiotic and biotic drivers, respectively. More seriously, geogenic As accelerated the prevalence of high-risk ARGs and multidrug-resistant bacteria. Our findings highlight the significance of geogenic As-induced co-selection for antibiotic resistance in groundwater and the hidden role of geogenic metals/metalloids in increasing antibiotic resistance. This study provides a basis for groundwater management of both high As and ARGs for human health., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The presence and accumulation of both, plastics and antibiotics in soils may lead to the colonization, selection, and propagation of soil bacteria with certain metabolic traits, e.g., antibiotic resistance, in the plastisphere. However, the impact of plastic-antibiotic tandem on the soil ecosystem functioning, particularly on microbial function and metabolism remains currently unexplored. Herein, we investigated the competence of soil bacteria to colonize plastics and degrade 13 C-labeled sulfamethoxazole (SMX). Using single-cell imaging, isotope tracers, soil respiration and SMX mineralization bulk measurements we show that microbial colonization of polyethylene (PE) and polystyrene (PS) surfaces takes place within the first 30 days of incubation. Morphologically diverse microorganisms were colonizing both plastic types, with a slight preference for PE substrate. CARD-FISH bacterial cell counts on PE and PS surfaces formed under SMX amendment ranged from 5.36 × 10 3 to 2.06 × 10 4 , and 2.06 × 10 3 to 3.43 × 10 3 hybridized cells mm -2 , respectively. Nano-scale Secondary Ion Mass Spectrometry measurements show that 13 C enrichment was highest at 130 days with values up to 1.29 atom%, similar to those of the 13 CO 2 pool (up to 1.26 atom%, or 22.55 ‰). Independent Mann-Whitney U test showed a significant difference between the control plastisphere samples incubated without SMX and those in 13 C-SMX incubations (P < 0.001). Our results provide direct evidence demonstrating, at single-cell level, the capacity of bacterial colonizers of plastics to assimilate 13 C-SMX from contaminated soils. These findings expand our knowledge on the role of soil-seeded plastisphere microbiota in the ecological functioning of soils impacted by anthropogenic stressors., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Global patterns in soil microbiomes are driven by non-linear environmental thresholds. Fertilization is known to shape the soil microbiome of terrestrial ecosystems worldwide. Yet, whether fertilization influences global thresholds in soil microbiomes remains virtually unknown. Here, utilizing optimized machine learning models with Shapley additive explanations on a dataset of 10,907 soil samples from 24 countries, we discovered that the microbial community response to fertilization is highly dependent on environmental contexts. Furthermore, the interactions among nitrogen (N) addition, pH, and mean annual temperature contribute to non-linear patterns in soil bacterial diversity. Specifically, we observed positive responses within a soil pH range of 5.2-6.6, with the influence of higher temperature (>15°C) on bacterial diversity being positive within this pH range but reversed in more acidic or alkaline soils. Additionally, we revealed the threshold effect of soil organic carbon and total nitrogen, demonstrating how temperature and N addition amount interacted with microbial communities within specific edaphic concentration ranges. Our findings underscore how complex environmental interactions control soil bacterial diversity under fertilization., (© 2024 John Wiley & Sons Ltd.)

Human activities have profoundly altered the Earth's phosphorus (P) cycling process and its associated microbial communities, yet their global distribution pattern and response to human influences remain unclear. Here, we estimated the abundances of P-cycling genes from 3321 global soil metagenomic samples and mapped the global distribution of five key P-cycling processes, that is, organic phosphoester hydrolysis, inorganic phosphorus solubilization, two-component system, phosphotransferase system, and transporters. Structural equation modeling and random forest analysis were employed to assess the impact of anthropogenic and environmental factors on the abundance of P-cycling genes. Our findings suggest that although less significant than the climate and soil profile, human-related factors, such as economic activities and population, are important drivers for the variations in P-cycling gene abundance. Notably, the gene abundances were increased parallel to the extent of human intervention, but generally at low and moderate levels of human activities. Furthermore, we identified critical genera, such as Pseudomonas and Lysobacter, which were sensitive to the changes in human activities. This study provides insights into the responses of P-cycling microbes to human activities at a global scale, enhancing our understanding of soil microbial P cycling and underscoring the importance of sustainable human activities in the Earth's biogeochemical cycle., (© 2024 John Wiley & Sons Ltd.)

The study of the fractions and distribution characteristics of organic phosphorus in the sediment of the water level fluctuating zone of Nansi Lake is conducive to revealing the transformation of phosphorus in the lake, and has important scientific significance for controlling the eutrophication of Nansi Lake. Based on the sediment of the water level fluctuation zone of Nansi Lake. The improved Hedley continuous grading extraction, ultraviolet-visible spectroscopy and three-dimensional fluorescence spectroscope were used to characterize the structural characteristics and stability of organic molecules in the sediment, and to reflect the differences in the structure and stability of organophosphate in the water level fluctuating zone. Principal component analysis (PCA), Redundancy analysis (RDA) and correlation heat map analysis were used to analyze the correlation between phosphorus and physicochemical index. The results showed that the alternation between wet-dry conditions was more favorable for the release of phosphorus from sediment, compared to continuous inundation conditions. Moreover, the higher the frequency of wet-dry alternations, the greater the release of phosphorus in different forms from the sediment. Wet-dry alternation resulted in a reduction of substituent on the aromatic rings of sediment DOM (dissolved organic matter), and the continuous drying would increase the molecular weight and humidification degree of DOM in the sediment. Correlation analysis showed that NaOH-P o content in sediment was significantly negatively correlated with TP, IP, OP and various organophosphorus forms, indicating a close transformation relationship between phosphorus forms in sediment. The results can provide a scientific basis for controlling the release of endogenous phosphorus and the risk of eutrophication in Nansi Lake., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Natural environments play a crucial role in transmission of antimicrobial resistance (AMR). Development of methods to manage antibiotic resistance genes (ARGs) in natural environments are usually limited to the laboratory or field scale, partially due to the complex dynamics of transmission between different environmental compartments. Here, we conducted a nine-year longitudinal profiling of ARGs at a watershed scale, and provide evidence that restrictions on livestock farms near water bodies significantly reduced riverine ARG abundance. Substantial reductions were revealed in the relative abundance of genes conferring resistance to aminoglycosides (42%), MLSB (36%), multidrug (55%), tetracyclines (53%), and other gene categories (59%). Additionally, improvements in water quality were observed, with distinct changes in concentrations of dissolved reactive phosphorus, ammonium, nitrite, pH, and dissolved oxygen. Antibiotic residues and other pharmaceuticals and personal care products (PPCPs) maintain at a similarly low level. Microbial source tracking demonstrates a significant decrease in swine fecal indicators, while human fecal pollution remains unchanged. These results suggest that the reduction in ARGs was due to a substantial reduction in input of antibiotic resistant bacteria and genes from animal excreta. Our findings highlight the watershed as a living laboratory for understanding the dynamics of AMR, and for evaluating the efficacy of environmental regulations, with implications for reducing environmental risks associated with AMR on a global scale., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Microbially-mediated arsenic biotransformation plays a pivotal role in the biogeochemical cycling of arsenic; however, the presence of arsenic biotransformation genes (ABGs) in urban dust remains unclear. To investigate the occurrence and spatiotemporal distributions of ABGs, a total of one hundred and eighteen urban dust samples were collected from different districts of Xiamen city, China in summer and winter. Although inorganic arsenic species, including arsenate [As(V)] and arsenite [As(III)], were found to be predominant, the methylated arsenicals, particularly trimethylarsine oxide [TMAs(V)O] and dimethylarsenate [DMAs(V)], were detected in urban dust. Abundant ABGs were identified in urban dust via AsChip analysis (a high-throughput qPCR chip for ABGs), of which As(III) S-adenosylmethionine methyltransferase genes (arsM), As(V) reductase genes (arsC), As(III) oxidase genes (aioA), As(III) transporter genes (arsB), and arsenic-sensing regulator genes (arsR) were the most prevalent, collectively constituting more than 90 % of ABGs in urban dust. Microbes involved in arsenic methylation were assigned to bacteria (e.g., Actinomycetes and Alphaproteobacteria), archaea (e.g., Halobacteria), and eukaryotes (e.g., Chlamydomonadaceae) in urban dust via the arsM amplicon sequencing. Temperature, a season-dependent environmental factor, profoundly affected the abundance of ABGs and the composition of microbes involved in arsenic methylation. This study provides new insights into the presence of ARGs within the urban dust., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Phosphate-solubilizing bacteria (PSB) are crucial for enhancing phosphorus bioavailability and regulating phosphorus transformation processes. However, the in situ phosphorus-solubilizing activity and the link between phenotypes and genotypes for PSB remain unidentified. Here we employed single-cell Raman spectroscopy combined with heavy water to discern and quantify soil active PSB. Our results reveal that PSB abundance and in situ activity differed significantly between soil types and fertilization treatments. Inorganic fertilizer input was the key driver for active PSB distribution. Targeted single-cell sorting and metagenomic sequencing of active PSB uncovered several low-abundance genera that are easily overlooked within bulk soil microbiota. We elucidate the underlying functional genes and metabolic pathway, and the interplay between phosphorus and carbon cycling involved in high phosphorus solubilization activity. Our study provides a single-cell approach to exploring PSB from native environments, enabling the development of a microbial solution for the efficient agronomic use of phosphorus and mitigating the phosphorus crisis., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Cardiopulmonary progenitor cells (CPPs) constitute a minor subpopulation of cells that are commonly associated with heart and lung morphogenesis during embryonic development but completely subside after birth. This fact offers the possibility for the treatment of pulmonary heart disease (PHD), in which the lung and heart are both damaged. A reliable source of CPPs is urgently needed. In this study, we reprogrammed human cardiac fibroblasts (HCFs) into CPP-like cells (or induced CPPs, iCPPs) and evaluated the therapeutic potential of iCPP-derived exosomes for acute lung injury (ALI). iCPPs were created in passage 3 primary HCFs by overexpressing GLI1, WNT2, ISL1 and TBX5 (GWIT). Exosomes were isolated from the culture medium of passage 6-8 GWIT-iCPPs. A mouse ALI model was established by intratracheal instillation of LPS. Four hours after LPS instillation, ALI mice were treated with GWIT-iCPP-derived exosomes (5 × 10 9 , 5 × 10 10 particles/mL) via intratracheal instillation. We showed that GWIT-iCPPs could differentiate into cell lineages, such as cardiomyocyte-like cells, endothelial cells, smooth muscle cells and alveolar epithelial cells, in vitro. Transcription analysis revealed that GWIT-iCPPs have potential for heart and lung development. Intratracheal instillation of iCPP-derived exosomes dose-dependently alleviated LPS-induced ALI in mice by attenuating lung inflammation, promoting endothelial function and restoring capillary endothelial cells and the epithelial cells barrier. This study provides a potential new method for the prevention and treatment of cardiopulmonary injury, especially lung injury, and provides a new cell model for drug screening., (© 2024. The Author(s), under exclusive licence to Shanghai Institute of Materia Medica, Chinese Academy of Sciences and Chinese Pharmacological Society.)

The estuarine plastisphere, a novel ecological habitat in the Anthropocene, has garnered global concerns. Recent geochemical evidence has pointed out its potential role in influencing nitrogen biogeochemistry. However, the biogeochemical significance of the plastisphere and its mechanisms regulating nitrogen cycling remain elusive. Using 15 N- and 13 C-labelling coupled with metagenomics and metatranscriptomics, here we unveil that the plastisphere likely acts as an underappreciated nitrifying niche in estuarine ecosystems, exhibiting a 0.9 ~ 12-fold higher activity of bacteria-mediated nitrification compared to surrounding seawater and other biofilms (stone, wood and glass biofilms). The shift of active nitrifiers from O 2 -sensitive nitrifiers in the seawater to nitrifiers with versatile metabolisms in the plastisphere, combined with the potential interspecific cooperation of nitrifying substrate exchange observed among the plastisphere nitrifiers, collectively results in the unique nitrifying niche. Our findings highlight the plastisphere as an emerging nitrifying niche in estuarine environment, and deepen the mechanistic understanding of its contribution to marine biogeochemistry., (© 2024. The Author(s).)

International arsenic trade, physical and virtual, has resulted in considerable transfer of arsenic pollution across regions. However, no study has systematically captured, estimated, and compared physical and virtual arsenic trade and its relevant impacts. This study combines material flow analysis and embodied emission factors to estimate embedded (including direct and indirect trade) and embodied arsenic trade during 1990-2019, encompassing 18 arsenic-containing products among 244 countries. Global embedded arsenic trade increased considerably from 47 ± 7.3 to 450 ± 68 kilotonnes (kt) during this time and was dominated by indirect arsenic trade, contributing 94 and 90% to global arsenic trade in 1990 and 2019, respectively. Since the 1990s, global arsenic trade centers and the main flows have shifted from European and American markets to developing countries. The mass of arsenic involved in embodied trade increased from 87.5 ± 26 kt in 1990 to 800 ± 236 kt in 2019. Direct trade and indirect trade aggravate arsenic environmental emissions in major importing countries, like China, while embodied trade aggravates arsenic environmental emissions in major exporting countries, like Peru and Chile. The trade-related arsenic pollution transfer calls for a rational arsenic emission responsibility-sharing mechanism and corresponding policy recommendations for different trading countries.

Antibiotic resistance genes (ARGs) have moved into focus as a critically important response variable in global change biology, given the increasing environmental and human health threat posed by these genes. However, we propose that elevated levels of ARGs should also be considered a factor of global change, not just a response. We provide evidence that elevated levels of ARGs are a global change factor, since this phenomenon is linked to human activity, occurs globally, and affects biota. We explain why ARGs could be considered the global change factor, rather than the organisms containing them; and we highlight the difference between ARGs and the presence of antibiotics, which are not necessarily linked since elevated levels of ARGs are caused by multiple factors. Importantly, shifting the perspective to elevated levels of ARGs as a factor of global change opens new avenues of research, where ARGs can be the experimental treatment. This includes asking questions about how elevated ARG levels interact with other global change factors, or how ARGs influence ecosystem processes, biodiversity or trophic relationships. Global change biology stands to profit from this new framing in terms of capturing more completely the real extent of human impacts on this planet., (© 2024 John Wiley & Sons Ltd.)

Conversion from natural lands to cropland, primarily driven by agricultural expansion, could significantly alter soil microbiome worldwide; however, influences of forest-to-cropland conversion on microbial hierarchical interactions and ecosystem multifunctionality have not been fully understood. Here, we examined the effects of forest-to-cropland conversion on intratrophic and cross-trophic microbial interactions and soil ecosystem multifunctionality and further disclosed their underlying drivers at a national scale, using Illumina sequencing combined with high-throughput quantitative PCR techniques. The forest-to-cropland conversion significantly changed the structure of soil microbiome (including prokaryotic, fungal, and protistan communities) while it did not affect its alpha diversity. Both intrakingdom and interkingdom microbial networks revealed that the intratrophic and cross-trophic microbial interaction patterns generally tended to be more modular to resist environmental disturbance introduced from forest-to-cropland conversion, but this was insufficient for the cross-trophic interactions to maintain stability; hence, the protistan predation behaviors were still disturbed under such conversion. Moreover, key soil microbial clusters were declined during the forest-to-cropland conversion mainly because of the increased soil total phosphorus level, and this drove a great degradation of the ecosystem multifunctionality (by 207%) in cropland soils. Overall, these findings comprehensively implied the negative effects of forest-to-cropland conversion on the agroecosystem, from microbial hierarchical interactions to ecosystem multifunctionality.

Xylem serves as a conduit linking soil to the aboveground plant parts and facilitating the upward movement of microbes into leaves and fruits. Despite this potential, the composition of the xylem microbiome and its associated risks, including antibiotic resistance, are understudied. Here, we cultivated tomatoes and analyzed their xylem sap to assess the microbiome and antibiotic resistance profiles following treatment with sewage sludge. Our findings show that xylem microbes primarily originate from soil, albeit with reduced diversity in comparison to those of their soil microbiomes. Using single-cell Raman spectroscopy coupled with D 2 O labeling, we detected significantly higher metabolic activity in xylem microbes than in rhizosphere soil, with 87% of xylem microbes active compared to just 36% in the soil. Additionally, xylem was pinpointed as a reservoir for antibiotic resistance genes (ARGs), with their abundance being 2.4-6.9 times higher than in rhizosphere soil. Sludge addition dramatically increased the abundance of ARGs in xylem and also increased their mobility and host pathogenicity. Xylem represents a distinct ecological niche for microbes and is a significant reservoir for ARGs. These results could be used to manage the resistome in crops and improve food safety.

Antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) coexist in organic fertilized agroecosystems based on their correlations in abundance, yet evidence for the genetic linkage of ARG-MRGs co-selected by organic fertilization remains elusive. Here, an analysis of 511 global agricultural soil metagenomes reveals that organic fertilization correlates with a threefold increase in the number of diverse types of ARG-MRG-carrying contigs (AMCCs) in the microbiome (63 types) compared to non-organic fertilized soils (22 types). Metatranscriptomic data indicates increased expression of AMCCs under higher arsenic stress, with co-regulation of the ARG-MRG pairs. Organic fertilization heightens the coexistence of ARG-MRG in genomic elements through impacting soil properties and ARG and MRG abundances. Accordingly, a comprehensive global map was constructed to delineate the distribution of coexistent ARG-MRGs with virulence factors and mobile genes in metagenome-assembled genomes from agricultural lands. The map unveils a heightened relative abundance and potential pathogenicity risks (range of 4-6) for the spread of coexistent ARG-MRGs in Central North America, Eastern Europe, Western Asia, and Northeast China compared to other regions, which acquire a risk range of 1-3. Our findings highlight that organic fertilization co-selects genetically linked ARGs and MRGs in the global soil microbiome, and underscore the need to mitigate the spread of these co-resistant genes to safeguard public health., (© 2024. The Author(s).)

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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

The rhizosphere influence on the soil microbiome and function of crop wild progenitors (CWPs) remains virtually unknown, despite its relevance to develop microbiome-oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence-a comparison between rhizosphere and bulk soil samples-on bacterial, fungal, protists and invertebrate communities and on soil multifunctionality across nine CWPs at their sites of origin. Overall, rhizosphere influence was higher for abundant taxa across the four microbial groups and had a positive influence on rhizosphere soil organic C and nutrient contents compared to bulk soils. The rhizosphere influence on abundant soil microbiomes was more important for soil multifunctionality than rare taxa and environmental conditions. Our results are a starting point towards the use of CWPs for rhizosphere engineering in modern crops., (© 2024 The Author(s). Ecology Letters published by John Wiley & Sons Ltd.)

Microbial communities play a crucial role in ocean ecology and global biogeochemical processes. However, understanding the intricate interactions among diversity, taxonomical composition, functional traits, and how these factors respond to climate change remains a significant challenge. Here, we propose seven distinct ecological statuses by systematically considering the diversity, structure, and biogeochemical potential of the ocean microbiome to delineate their biogeography. Anthropogenic climate change is expected to alter the ecological status of the surface ocean by influencing environmental conditions, particularly nutrient and oxygen contents. Our predictive model, which utilizes machine learning, indicates that the ecological status of approximately 32.44% of the surface ocean may undergo changes from the present to the end of this century, assuming no policy interventions. These changes mainly include poleward shifts in the main taxa, increases in photosynthetic carbon fixation and decreases in nutrient metabolism. However, this proportion can decrease significantly with effective control of greenhouse gas emissions. Our study underscores the urgent necessity for implementing policies to mitigate climate change, particularly from an ecological perspective., (© 2024. The Author(s).)

A myriad of nonantibiotic compounds is released into the environment, some of which may contribute to the dissemination of antimicrobial resistance by stimulating conjugation. Here, we analyzed a collection of studies to (i) identify patterns of transfer stimulation across groups and concentrations of chemicals, (ii) evaluate the strength of evidence for the proposed mechanisms behind conjugal stimulation, and (iii) examine the plausibility of alternative mechanisms. We show that stimulatory nonantibiotic compounds act at concentrations from 1/1000 to 1/10 of the minimal inhibitory concentration for the donor strain but that stimulation is always modest (less than 8-fold). The main proposed mechanisms for stimulation via the reactive oxygen species/SOS cascade and/or an increase in cell membrane permeability are not unequivocally supported by the literature. However, we identify the reactive oxygen species/SOS cascade as the most likely mechanism. This remains to be confirmed by firm molecular evidence. Such evidence and more standardized and high-throughput conjugation assays are needed to create technologies and solutions to limit the stimulation of conjugal gene transfer and contribute to mitigating global antibiotic resistance.

Global riverine nitrous oxide (N 2 O) emissions have increased more than 4-fold in the last century. It has been estimated that the hyporheic zones in small streams alone may contribute approximately 85% of these N 2 O emissions. However, the mechanisms and pathways controlling hyporheic N 2 O production in stream ecosystems remain unknown. Here, we report that ammonia-derived pathways, rather than the nitrate-derived pathways, are the dominant hyporheic N 2 O sources (69.6 ± 2.1%) in agricultural streams around the world. The N 2 O fluxes are mainly in positive correlation with ammonia. The potential N 2 O metabolic pathways of metagenome-assembled genomes (MAGs) provides evidence that nitrifying bacteria contain greater abundances of N 2 O production-related genes than denitrifying bacteria. Taken together, this study highlights the importance of mitigating agriculturally derived ammonium in low-order agricultural streams in controlling N 2 O emissions. Global models of riverine ecosystems need to better represent ammonia-derived pathways for accurately estimating and predicting riverine N 2 O emissions., (© 2024. The Author(s).)

The global health crisis posed by increasing antimicrobial resistance (AMR) implicitly requires solutions based a One Health approach, yet multisectoral, multidisciplinary research on AMR is rare and huge knowledge gaps exist to guide integrated action. This is partly because a comprehensive survey of past research activity has never performed due to the massive scale and diversity of published information. Here we compiled 254,738 articles on AMR using Artificial Intelligence (AI; i.e., Natural Language Processing, NLP) methods to create a database and information retrieval system for knowledge extraction on research perfomed over the last 20 years. Global maps were created that describe regional, methodological, and sectoral AMR research activities that confirm limited intersectoral research has been performed, which is key to guiding science-informed policy solutions to AMR, especially in low-income countries (LICs). Further, we show greater harmonisation in research methods across sectors and regions is urgently needed. For example, differences in analytical methods used among sectors in AMR research, such as employing culture-based versus genomic methods, results in poor communication between sectors and partially explains why One Health-based solutions are not ensuing. Therefore, our analysis suggest that performing culture-based and genomic AMR analysis in tandem in all sectors is crucial for data integration and holistic One Health solutions. Finally, increased investment in capacity development in LICs should be prioritised as they are places where the AMR burden is often greatest. Our open-access database and AI methodology can be used to further develop, disseminate, and create new tools and practices for AMR knowledge and information sharing., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Arbuscular mycorrhizal (AM) fungi play an important role in soil organic matter (SOM) formation and stabilization. Previous studies have emphasized organic compounds produced by AM fungi as persistent binding agents for aggregate formation and SOM storage. This concept overlooks the multiple biogeochemical processes mediated by AM fungal activities, which drive SOM generation, reprocessing, reorganization, and stabilization. Here, we propose an updated conceptual framework to facilitate a mechanistic understanding of the role of AM fungi in SOM dynamics. In this framework, four pathways for AM fungi-mediated SOM dynamics are included: 'Generating', AM fungal exudates and biomass serve as key sources of SOM chemodiversity; 'Reprocessing', hyphosphere microorganisms drive SOM decomposition and resynthesis; 'Reorganizing', AM fungi mediate soil physical changes and influence SOM transport, redistribution, transformation, and storage; and 'Stabilizing', AM fungi drive mineral weathering and organo-mineral interactions for SOM stabilization. Moreover, we discuss the AM fungal role in SOM dynamics at different scales, especially when translating results from small scales to complex larger scales. We believe that working with this conceptual framework can allow a better understanding of AM fungal role in SOM dynamics, therefore facilitating the development of mycorrhiza-based technologies toward soil health and global change mitigation., (© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation.)