土壤微塑料或其他废弃物上的抗生素抗性基因随时间变化的研究

Intensive facility agriculture is increasingly threatened by the co-occurrence of heavy metals (HMs), micro-/nano plastics (MNPs), and antibiotic resistance genes (ARGs), yet effective strategies for mitigating ternary composite pollution remain limited. Here, a five-year field trail was conducted to evaluate the imparts of different fertilization regimes on the occurrence, interaction, and mitigation of composite pollution in facility agricultural soils, with a particular attention on the co-application of biochar and organic fertilizer. The results showed that conventional fertilization exacerbated the accumulation and synergistic risks of HMs, MNPs, and ARGs, whereas its co-applied with biochar significantly reduced individual pollutant loads and lowered the comprehensive ternary pollution index by 28.0-62.2 %. Variance partitioning and structural equation modeling revealed that microbial community structure played a dominant role in regulating composite pollution, exceeding the contribution of soil physicochemical properties. The biochar-organic fertilizer amendment reshaped microbial community assembly by narrowing ecological niche breadth, enhancing community stability, which primarily drove a targeted enrichment of functional taxa (e.g. Nitrospira, Sphingopyxis, Hydrogenophaga, and Steroidobacter) involved in microplastic degradation and heavy metal immobilization, concurrently suppressing ARGs host populations. Metagenomic analyses indicated a dual-level regulation of microbial carbon metabolism. The treatment enhanced fermentation-driven, energy-efficient carbon conversion pathways in functional microbes responsible for plastic degradation and metal immobilization, while concurrently inhibiting carbon fixation-dependent metabolic functions in ARG-associated hosts, thereby reducing their ecological competitiveness. Overall, this study highlights carbon resource-driven microbial metabolic differentiation as a central mechanism for the synergistic mitigation of complex soil pollution and provides a practical fertilization strategy for sustainable pollution control in protected agricultural systems.

Microplastics (MPs) and antibiotic resistance genes (ARGs) are two types of contaminants that are widely present in the soil environment. MPs can act as carriers of microbes, facilitating the colonization and spread of ARGs and thus posing potential hazards to ecosystem safety and human health. In the present study, we explored the microbial networks and ARG distribution characteristics in different soil types (heavy metal (HM)-contaminated soil and agricultural soil planted with different plants: Bidens pilosa L., Ipomoea aquatica F., and Brassica chinensis L.) after the application of MPs and evaluated environmental factors, potential microbial hosts, and ARGs. The microbial communities in the three rhizosphere soils were closely related to each other, and the modularity of the microbial networks was greater than 0.4. Moreover, the core taxa in the microbial networks, including Actinobacteriota, Proteobacteria, and Myxococcota, were important for resisting environmental stress. The ARG resistance mechanisms were dominated by antibiotic efflux in all three rhizosphere soils. Based on the annotation results, the MP treatments induced changes in the relative abundance of microbes carrying ARGs, and the G1-5 treatment significantly increased the abundance of MuxB in Verrucomicrobia, Elusimicrobia, Actinobacteria, Planctomycetes, and Acidobacteria. Path analysis showed that changes in MP particle size and dosage may indirectly affect soil enzyme activities by changing pH, which affects microbes and ARGs. We suggest that MPs may provide surfaces for ARG accumulation, leading to ARG enrichment in plants. In conclusion, our results demonstrate that MPs, as potentially persistent pollutants, can affect different types of soil environments and that the presence of ARGs may cause substantial environmental risks.

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The widespread prevalence of microplastics (MPs) in the environment poses concerns as they are vectors of antibiotic resistance genes (ARGs). The relationships between antibiotic resistomes and MPs remain unexplored in soil which was considered as the reservoirs of MPs and ARGs. This study investigated the effects of polyvinyl chloride (PVC) MPs on soil bacterial communities and ARG abundance which soil samples sourced from 20 provinces across China. We found that PVC significantly influences soil bacterial community structure and ARG abundance. Structural equation modeling revealed that PVC alters soil characteristics, ultimately affecting soil bacterial communities, including ARG-containing bacterial hosts, and the relative abundance of ARGs. This study enhances our understanding of how MPs influence the proliferation and hosts of ARGs within diverse soil environments, offering crucial insights for future strategies in plastic management and disposal.

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Concerns about the ecological safety of both conventional and biodegradable microplastics have grown due to the inadequate end-of-life treatments of plastics. In this study, the effects of conventional and biodegradable microplastics on the spread of antibiotic resistance genes (ARGs) and virulence factors (VFs) were estimated in a soil microcosm experiment. The gene profiles and their respective bacterial hosts in soil were evaluated by metagenomic sequencing methods. The abundances of ARGs and VFs in polybutylene succinate (PBS) treated soils were statistically higher than the values in the control and conventional microplastic treatments. In comparison with the control, application of conventional microplastics showed negligible effects on ARG and VF profiles in the soil, while biodegradable microplastic amendments significantly changed the compositions of ARGs and VFs. The host-tracking analysis suggested application of microplastics broadened the bacterial hosts of ARGs and VFs in the soil. The percentage of Proteobacteria as ARG hosts increased from 38.5% in the control soils to 58.2% in microplastic exposed soil. The genus Bradyrhizobium was the dominant host of ARGs and VFs in biodegradable microplastic treatments, while conventional microplastics increased the percentages of Pseudomonas as the bacterial hosts. This study enhances the understanding of the effects of conventional and biodegradable microplastics on the propagation and hosts of ARGs and VFs in the terrestrial environment, providing essential insights into the risk assessment and management of plastics.

This is the first study investigating the effects of freeze-thaw (FT) and microplastics (MPs) on the distribution of antibiotic resistance genes (ARGs) in soil aggregates (i.e., soil basic constituent and functional unit) via microcosm experiments. The results showed that FT significantly increased the total relative abundance of target ARGs in different aggregates due to the increase in intI1 and ARG host bacteria. However, polyethylene MPs (PE-MPs) hindered the increase in ARG abundance caused by FT. The host bacteria carrying ARGs and intI1 varied with aggregate size, and the highest number of hosts was observed in micro-aggregates (<0.25 mm). FT and MPs altered host bacteria abundance by affecting aggregate physicochemical properties and bacterial community and enhanced multiple antibiotic resistance via vertical gene transfer. Although the dominant factors affecting ARGs varied with aggregate size, intI1 was a co-dominant factor in various-sized aggregates. Furthermore, other than ARGs, FT, PE-MPs, and their integration promoted the proliferation of human pathogenic bacteria in aggregates. These findings suggested that FT and its integration with MPs significantly affected ARG distribution in soil aggregates. They amplified antibiotic resistance environmental risks, contributing to a profound understanding of soil antibiotic resistance in the boreal region.

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The differential effects of microplastics and phthalates released from microplastics on antibiotic resistance genes in soil remain unknown. This study aims to analyze the varying characteristics and driving mechanisms of antibiotic resistance genes in soils amended with high-density polyethylene microplastics (with and without phthalates) through a 60-day microcosm experiment. The results indicate that the amended high-density polyethylene microplastics (containing phthalates) enhanced the abundance of antibiotic resistance genes in the soil, a phenomenon that markedly increased with the amendment period. Nevertheless, the addition of high-density polyethylene microplastics (without phthalates) mitigated the abundance of antibiotic resistance genes, which was less significant with increasing amendment period. Furthermore, addition of high-density polyethylene microplastics altered the soil properties, especially porosity. The phthalates released from high-density polyethylene microplastics and the changes in the soil properties transformed soil bacterial communities, resulting in increased abundance of bacterial hosts harboring antibiotic resistance genes (Calditrichaeota, Candidate division CPR1, Candidatus Delongbacteria, Candidatus Kapabacteria, Candidatus Spechtbacteria, Candidatus Wildermuthbacteria, and Ignavibacteriae), thereby enhancing the abundance of antibiotic resistance genes. These findings suggest that compared to microplastics, the phthalates released from microplastics considerably affect the antibiotic resistance genes in soils, thereby promoting the propagation of antibiotic resistance genes in agricultural environments.

The impact of microplastics on antibiotic resistance has attracted widespread attention. However, previous studies primarily focused on the effects of individual microplastics. In reality, diverse microplastic types accumulate in soil, and it remains less well studied whether microplastic diversity (i.e., variations in color, shape or polymer type) can be an important driver of increased antibiotic resistance gene (ARG) abundance. Here, we employed microcosm studies to investigate the effects of microplastic diversity on soil ARG dynamics through metagenomic analysis. Additionally, we evaluated the associated potential health risks by profiling virulence factor genes (VFGs) and mobile genetic elements (MGEs). Our findings reveal that as microplastic diversity increases, there is a corresponding rise in the abundance of soil ARGs, VFGs and MGEs. We further identified microbial adaptive strategies involving genes (changed genetic diversity), community (increased specific microbes), and functions (enriched metabolic pathways) that correlate with increased ARG abundance and may thus contribute to ARG dissemination. Additional global change factors, including fungicide application and plant diversity reduction, also contributed to elevated ARG abundance. Our findings suggest that, in addition to considering contamination levels, it is crucial to monitor microplastic diversity in ecosystems due to their potential role in driving the dissemination of antibiotic resistance through multiple pathways. The effects of microplastics (MPs) on soil microbial communities and antimicrobial resistance genes are not well understood. Here, the authors used microcosm studies to show that MP diversity, and partially fungicide treatment and reduced plant diversity, correlate with higher levels of ARG and related genetic factors.

Microplastics (MPs) pollution is a growing global environmental concern. MPs serve as ecological niches for microbial communities, which may accelerate the spread of antibiotic resistance genes (ARGs), posing risks to the breeding industry. While studies on MPs in aquatic organisms are common, research on farmed poultry is limited. This study investigates MPs in poultry farm environments and waterfowl intestines for the first time. MPs were isolated via density separation and analyzed for characterization in soil, pond water, and waterfowl intestines. Metagenomics was used to investigate the association between environment MPs colonized-microbiota and waterfowl gut microbiota. Our findings reveal that MPs are abundant in soil (6.75 ± 2.78 items/g d.w.), pond water (0.94 ± 0.28 items/g w.w.), and poultry intestines (45.35 ± 19.52 items/g w.w.), primarily appearing as fragmented particles sized 20-50 μm. MPs abundance in intestines correlates with environmental levels. Colonized-microbiota on MPs are linked to poultry intestinal microbiota, with greater diversity and microbial functions. Network analysis reveals that Corynebacterium plays a key role in MPs and poultry intestinal. Polymyxin resistance exhibits high clustering. Procrustes analysis reveals correlations between MPs, bacteria, and ARGs in the farming environment. Overall, MPs in poultry farms may facilitate pathogen and ARGs transmission, posing risks to animal gut health.

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Microplastics (MPs) and antibiotic resistance genes (ARGs) coexist widely in farmland soils, but the fate and abundance of ARGs on MPs is rarely explored. In this study, high-throughput fluorescent quantitative polymerase chain reaction was used to determine ARGs on MPs in facility vegetable soil. The results indicated that when the particle size of the MPs was larger, the weathering was more serious, or the MPs came from soils with a long vegetable cultivation period, the levels of antibiotics and heavy metals on the MPs were higher. The distribution of the detected ARGs types on distinct MPs showed changes. Compared with weakly weathered MPs, the detected beta lactamase and aminoglycoside resistance genes on strongly weathered MPs were decreased by 2.6% and 1.7%, while the detected sul-ARGs and Macrolide-Lincosamide-Streptogramin B (MLSB) resistance genes were increased by 1.5% and 2.8%. Compared with smaller MPs, the detected MLSB and vancomycin resistance genes on larger MPs were decreased by 2.0% and 1.4%, while the detected fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol (FCA) resistance genes and sul-ARGs were increased by 1.2% and 1.0%. Compared with MPs in soil after three years of vegetable cultivation, the detected FCA resistance genes and sul-ARGs on MPs in soil after ten years of vegetable cultivation were decreased by 1.3% and 1.6%, while the detected beta lactamase and aminoglycoside resistance genes were increased by 1.0% and 1.7%. This study suggests that MPs with larger size, stronger weathering or from soil after long-term vegetable cultivation adsorb more antibiotics and heavy metals and cause more mobile genetic elements, which can contribute to antibiotic resistance on the MPs.

The prolonged application of mulch and manure in agriculture has led to significant microplastic (MP) pollution in fertilized soils, raising global concerns about its potential impacts on soil health and ecosystem function. However, the effects of MP exposure on antibiotic resistance genes (ARGs) and microbial communities in fertilized soils are unknown. Therefore, we comprehensively explored the trends and drivers of ARGs during their natural abatement under the stress of conventional and biodegradable MP addition in fertilized soils using a soil microcosm experiment and metagenomic. The findings indicated that the presence of polybutylene succinate MPs (PBS-MPs) reduced the natural attenuation rate of ARGs in fertilized soils while increasing the fraction of high-risk ARGs in soils. Microbial communities and mobile genetic elements (MGEs) mainly drove the inhibitory effect of MPs on ARG abatement. Interestingly, most potential hosts for the coexistence of ARGs, metal resistance genes (MRGs), and MGEs were annotated as pathogens, such as Escherichia spp., Salmonella spp., and Klebsiella spp. In addition, MP stress in fertilized soil may lead to long-term contamination by highly virulent and antibiotic-resistant Escherichia coli. MPs influence the distribution of carbon sources, which in turn reduces the diversity and stability of soil microbial communities, while simultaneously promoting the colonization of crucial ARG hosts, like Dyella spp. This ultimately prolonged the high-risk state for ARG proliferation in the soil. This study highlights the significant risk posed by MPs to the persistence and spread of ARGs in fertilized soils. These results provide valuable insights for managing MP contamination in agricultural systems, emphasizing the need for sustainable practices to mitigate the long-term environmental risks associated with MP pollution.

The diffusion and distribution of ubiquitous microplastics and antibiotic resistance genes (ARGs) in soil ecosystems are easily influenced by earthworm activity. However, minimal research exists on the bidirectional dissemination of ARGs in the soil-earthworm ecosystems under microplastic stress. Focusing on the typical microplastic polyvinyl chloride (PVC) microspheres in simulated soil-earthworm (Eisenia fetida) systems, we characterized the PVC-triggered interactive transmission of ARGs between earthworm guts and their dwelling soils using shotgun metagenomics and qPCR methodologies. PVC exposure did not alter the diversity and relative abundance of ARGs in earthworm-uninoculated soils but significantly increased those in earthworm-inoculated soils. Meanwhile, the abundance of ARGs increased in the earthworm gut under PVC stress. Source tracking analysis showed a higher source proportion of soil-borne ARGs into earthworm gut under PVC treatments. Mechanistically, PVC-triggered increasing prevalence of ARGs was significantly related to both the bacterial community and mobile genetic elements-mediated horizontal transfer in the soils, whereas the bacterial community predominated the process in the earthworm guts. Overall, our findings reveal a PVC-triggered bidirectional transmission pattern of ARGs between earthworm guts and their dwelling soils and highlight the overlooked ecotoxicological risk of microplastics in soil-earthworm systems.

Microplastics (MPs) are currently receiving widespread attention worldwide, and their co-occurrence with antibiotics is unavoidable. However, our understanding of how protists respond to co-pollution and mediate antibiotic resistance genes (ARGs) profiles remains exceedingly limited, particularly within non-target animals' guts. To bridge these gaps, we investigated the individual and combined effects of polyethylene and sulfamethoxazole (SMZ) on microbial communities and ARGs in soil and earthworm guts. We found that the MP-SMZ combination significantly elevated the abundance and richness of ARGs in the soil and earthworm. Protistan compositions (particularly consumers) responded more strongly to pollutants than did bacterial and fungal communities, especially under combined pollution. Interkingdom cooccurrence network analysis revealed that protists had stronger and more effective interactions with the resistome in the earthworm guts, suggesting that the impact of these protists on ARGs compositional changes was potentially modulated through the "top-down" regulation of bacteria and fungi. Meta-cooccurrence networks further confirmed that protist-related networks had more keystone pollution-sensitive ASVs (psASVs) and these psASVs were mostly associated with protistan consumers. Our study highlights protists as promising agents for regulating and monitoring microbial functions, as well as the ecological risks of the antibiotic resistome associated with MPs and SMZ pollution in agricultural ecosystems.

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Magnetic biochars (MBCs) have been shown to inhibit the horizontal transfer of antibiotic resistance genes (ARGs) in soils, both with and without microplastics (MPs); however, the underlying molecular biological mechanisms remain unclear. This study examined the effects of MBCs and coexisting polybutylene adipate terephthalate microplastics (PBAT MPs) on the physiological characteristics of Serratia marcescens ZY01 (a host strain carrying the tet gene) and further investigated their relationships with the absolute abundance of the tet gene in soil. The results demonstrated that MBCs promoted prodigiosin synthesis in Serratia marcescens ZY01 by mediating the electron transfer process, the effect of which was further enhanced in the presence of PBAT MPs. In treatments without PBAT MPs, MBCs generally suppressed the production of both proteins and polysaccharides in the extracellular polymeric substances. In contrast, in treatments containing PBAT MPs, the protein content gradually decreased with decreasing iron-to-biochar ratios, while the polysaccharide content remained largely unchanged. MBCs also elevated intracellular ROS levels due to the increased oxidative stress, particularly in treatments with PBAT MPs. A positive correlation between intracellular ROS levels and cell membrane permeability indicates that intracellular ROS was the primary driver of the increased cell membrane permeability. The presence of MBCs and PBAT MPs generally provided favorable habitats for Serratia marcescens ZY01, thereby enhancing its cell viability. Mantel test analysis indicated that MBCs influenced Serratia growth in soil by modulating its cell viability. Furthermore, the increased intracellular ROS level was significantly positively correlated with the absolute abundance of the tet gene in soil, implying the horizontal transfer of the tet gene at the intra-genus level. These findings offer helpful insights for developing environmental remediation strategies based on biochar–iron composites.

Microplastics (MPs) in soil ecosystems significantly influence antibiotic resistance genes (ARGs) transmission and abundance. However, a holistic understanding of how MP characteristics interact with climatic and edaphic factors to drive ARGs fluctuations remain unclear. By integrating global metagenomic datasets, we compared divergence of soil microbial communities and antibiotic resistomes across MP types and applied interpretable machine learning (ML) techniques to explore ARG dynamics. Results revealed distinct microbial community and resistome patterns associated with MP types, explaining 31.0-36.2 % of the variation in bacterial structure and ARG profiles. Moreover, specific microbial biomarkers for 7 MP types underscore their significant role in structuring communities. Biodegradable MPs (e.g., polybutylene succinate, polyhydroxyalkanoates) exhibited reduced bacterial diversity but higher ARG abundance risk than conventional MPs. Among ML models, Gradient Boosted Decision Trees exhibited superior predictive performance for ARG abundance, with average R² values of 0.98 for training and 0.93 for testing. Driver importance analysis identified bacterial genera (mean contribution: 69.86 %) as the dominant factor in the abundance of primary ARG subtype, followed by climate (13.89 %), soil properties (9.55 %), and MP characteristics (6.70 %). This study provides novel insights into the environmental drivers of ARG dynamics in MP-contaminated soils, highlighting the importance of incorporating climate scenario projections into future ecological risk management strategies for MPs and ARGs.

Non-antibiotic chemicals in farmlands, including microplastics (MPs) and pesticides, have the potential to influence the soil microbiome and the dissemination of antibiotic resistance genes (ARGs). Despite this, there is limited understanding of the combined effects of MPs and pesticides on microbial communities and ARGs transmission in soil ecosystems. In this study, we observed that low-density polyethylene (LDPE) microplastic enhance the accumulation of pyraclostrobin in earthworms, resulting in reduced weight and causing severe oxidative damage. Analysis of 16 S rRNA amplification revealed that exposure to pyraclostrobin and/or LDPE disrupts the microbial community structure at the phylum and genus levels, leading to reduced alpha diversity in both the soil and earthworm gut. Furthermore, co-exposure to LDPE and pyraclostrobin increased the relative abundance of ARGs in the soil and earthworm gut by 2.15 and 1.34 times, respectively, compared to exposure to pyraclostrobin alone. It correlated well with the increasing relative abundance of genera carrying ARGs. Our findings contribute novel insights into the impact of co-exposure to MPs and pesticides on soil and earthworm microbiomes, highlighting their role in promoting the transfer of ARGs. This knowledge is crucial for managing the risk associated with the dissemination of ARGs in soil ecosystems.

This study examined the effects of polyethylene terephthalate (PET) nanoplastics on the rhizosphere of Oryza sativa L., focusing on dynamic changes and interactions among microbial communities, antibiotic resistance genes (ARGs) and microplastic degradation genes (MDGs). PET exposure altered the structure and function of soil microbial, enabling specific microbial groups to thrive in polluted environments. High-dose PET treatments markedly increased the abundance and dissemination of ARGs, primarily via resistance mechanisms such as antibiotic efflux and target alteration. By providing additional carbon sources and surfaces for microbial attachment, PET stimulated the growth of microorganisms harboring MDGs, resulting in an increase in MDGs abundance. The elevated expression of MDGs facilitated the propagation of ARGs, with overlapping host microorganisms suggesting that certain microbial groups exhibit dual metabolic capabilities, enabling them to endure both antibiotic and microplastic pressures. Toxic byproducts of microplastic degradation, such as mono-ethylhexyl phthalate, further promoted ARGs dissemination by increasing horizontal gene transfer frequency. Structural equation modeling revealed that PET indirectly influenced ARGs and MDGs expression by altering soil C/N ratio, available phosphorus, and enzyme activities. Thus, nanoscale PET exacerbates ecological risks to soil microbial communities by driving co-propagation of ARGs and MDGs, highlighting the persistent threat of composite pollution to agroecosystems.

The wide application of plastics has led to the ubiquitous presence of nanoplastics and microplastics in terrestrial environments. However, few studies have focused on the mechanism underlying the effects of plastic particles on soil microbiomes and resistomes, especially the differences between nanoplastics and microplastics. This study investigated the microbiome and resistome in soil exposed to polystyrene microplastics (mPS) or nanoplastics (nPS) through 16S rRNA and shotgun metagenomic sequencing. Distinct microbial communities were observed between mPS and nPS exposure groups, and nPS exposure significantly changed the bacterial composition even at the lowest amended rate (0.01%, w/w). The abundance of antibiotic resistance genes (ARGs) in nPS exposure (1%) was 0.26 copies per cell, significantly higher than that in control (0.21 copies per cell) and mPS exposure groups (0.21 copies per cell). It was observed that nanoplastics, bacterial community, and mobile genetic elements (MGEs) directly affected the ARG abundance in nPS exposure groups, while in mPS exposure groups, only MGEs directly induced the change of ARGs. Streptomyces was the predominant host for multidrug in the control and mPS exposure, whereas the primary host was changed to Bacillus in nPS exposure. Additionally, exposure to nPS induced several bacterial hosts to exhibit possible multi-antibiotic resistance characteristics. Our results indicated that the effects of plastic particles on the soil microbial community were size-dependent, and nano-sized plastic particles exhibited more substantial impacts. Both microplastics and nanoplastics promoted ARG transfer and diversified their bacterial hosts. These findings bear implications for the regulation of plastic waste and ARGs.

Microplastics (MPs) and antibiotic resistance genes (ARGs) are both enriched in soil-vegetable systems as a consequence of the prolonged use of agricultural mulches. MPs can form unique bacterial communities and provide potential hosts for ARGs. Therefore, MPs stress may promote the spread of ARGs from soil to crops. Increasing ARGs pollution in soil-vegetable system. In our research, we investigated the distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress. The results showed that MPs treatment decreased the relative abundance of ARGs in non-rhizosphere soil. High concentrations of MPs promoted the enrichment of tetracycline antibiotic resistance genes in rhizosphere soil. MPs treatment promoted the enrichment of ARGs and mobile genetic elements (MGEs) in lettuce tissues, and the overall abundance of ARGs in root after 0.5 %, 1 %, and 2 % (w/w, dry weight) polyethylene (PE) administration was considerably higher compared to that in the untreated group (p < 0.05). At the same time, high PE concentrations promoted the spread of sulfa ARGs from root to leaf. MPs also impacted the bacterial communities in the soil-plant system, and the changes in ARGs as well as MGEs in each part of the soil-vegetable system were significantly correlated with the bacterial diversity index (p < 0.05). Correlation analysis and network analysis showed that bacterial communities and MGEs were the main drivers of ARGs variation in soil-lettuce systems.

Effects of microplastics (MPs) and nanoplastics (NPs) on the spread of antibiotic resistance genes (ARGs) in soil-plant systems are still unclear. To investigate the spread and mechanisms of ARGs from soil to lettuce, lettuce was exposed to soil spiked with two environmentally relevant concentrations of polystyrene MPs (100 μm) and NPs (100 nm). Results showed that microorganisms that carried ARGs in soil were increased after exposure to MPs/NPs, which led to an increase in ARGs in roots. NPs were absorbed by roots and can be transported to leaves. Analysis of transcriptomics, proteomics and metabolomics indicated that high concentration of NPs regulated the expression of related genes and proteins and improved the accumulation of flavonoids in the lettuce, therefore decreased the abundance of microorganisms that contained ARGs. Our work emphasizes the size and dose influences of MPs and NPs on the spread of ARGs from soil to plant.

In the Anthropocene, increasing pervasive plastic pollution is creating a new environmental compartment, the plastisphere. How the plastisphere affects microbial communities and antibiotic resistance genes (ARGs) is an issue of global concern. Although this has been studied in aquatic ecosystems, our understanding of plastisphere microbiota in soil ecosystems remains poor. Here, we investigated plastisphere microbiota and ARGs of four types of microplastics (MPs) from diverse soil environments, and revealed effects of manure, temperature, and moisture on them. Our results showed that the MPs select for microbial communities in the plastisphere, and that these plastisphere communities are involved in diverse metabolic pathways, indicating that they could drive diverse ecological processes in the soil ecosystem. The relationship within plastisphere bacterial zero-radius operational taxonomic units (zOTUs) was predominantly positive, and neutral processes appeared to dominate community assembly. However, deterministic processes were more important in explaining the variance in ARGs in plastispheres. A range of potential pathogens and ARGs were detected in the plastisphere, which were enriched compared to the soil but varied across MPs and soil types. We further found that the addition of manure and elevation of soil temperature and moisture all enhance ARGs in plastispheres, and potential pathogens increase with soil moisture. These results suggested that plastispheres are habitats in which an increased potential pathogen abundance is spatially co-located with an increased abundance of ARGs under global change. Our findings provided new insights into the community ecology of the microbiome and antibiotic resistome of the soil plastisphere.

Soil serves as a major reservoir of both antibiotic resistance genes (ARGs) and microplastics. However, the characteristics of the antibiotic resistome in the soil plastisphere remain largely unknown. In this study, we used metagenomic approaches to reveal the changing patterns of ARGs and the bacterial community and their associations in response to three types of microplastics (light density polyethylene, LDPE; polypropylene, PP; polystyrene, PS) using particles 550 µm or 75 µm in diameter. The total ARG abundances significantly increased in the plastisphere and varied across plastic types. The LDPE plastisphere had the highest ARG total abundance and lowest Shannon diversity index, indicating that this plastic had the most severe negative impact on soil bacterial diversity. The PP plastisphere contained higher relative abundances of the pathogenic bacteria Acinetobacter johnsonii and Escherichia coli, demonstrating the higher pathogenic risk of the microbial communities enriched in the plastisphere. Specifically, multidrug resistance genes (ceoB and MuxB) co-existed with more than four microbial taxa, increasing the potential risk of ARG spread in pathogenic bacteria. These findings implied that the plastisphere acts as a hotspot for acquiring and spreading antibiotic resistance and may have long-term negative effects on the soil ecosystem and human health.

The complexity of soil microplastic pollution has driven deeper exploration of waste management strategies to evaluate environmental impact. This study introduced oversized microplastics (OMPs, 1-5 mm) during membrane composting to produce organic fertilizers, and conducted a 2 × 2 pot experiment: exogenous OMPs were added when normal fertilizer (no OMPs intervention) was applied, while artificial removal of OMPs was implemented when contaminated fertilizer (with OMPs) was used. The study assessed the effects of these management strategies on lettuce growth, soil environments, and potential biological safety risks related to the spread and expression of high-risk antibiotic resistance genes (ARGs) in humans. Results showed that both exogenous OMPs addition and removal negatively affected plant height and harvest index, with shifts in the rhizosphere microbial community identified as a key factor rather than soil nutrients. Exogenous OMPs altered rhizosphere and endophytic microbial communities, and plant growth-promoting bacteria were transferred to the surface of OMPs from rhizosphere soil. In contrast, bacteria such as Truepera, Pseudomonas, and Streptomyces in compost-derived OMPs supported lettuce growth, and their removal negated these effects. Some endophytic bacteria may promote growth but pose public health risks when transmitted through the food chain. OMPs in composting or planting significantly enhanced the expression of target ARGs in lettuce, particularly blaTEM. However, simulated digestion results indicated that OMPs reduced the expression of six key ARGs, including blaTEM, among the ten critical target ARGs identified in this context. Notably, the removal management strategies raised five of them posing potential risks from lettuce consumption. This study highlights that both introducing and removing OMPs may pose ecological and food safety risks, emphasizing the need for optimized organic waste management strategies to mitigate potential health hazards.

Current understanding on the fate and behavior of microplastics (MPs) in complex soil media remains inadequate. We characterized the aging and hetero-aggregation of a MP sampled in farmland soil, and explored its vertical downward transport in natural loamy sand. The MP was identified with FTIR spectrum as polypropylene, a plastic lighter than water. FTIR spectrum combined with SEM imaging confirmed the MP was highly aged, generating colloidal plastic fibers and carbonyl groups. SEM imaging coupled with EDX analysis suggested hetero-aggregation of the MP with soil minerals. Soil leaching tests performed with the clean MP (without soil minerals) (CMP), the raw MP (RMP) (with soil minerals), and the RMP with humic acid (HA) (RMP + HA) demonstrated that the mobility was insignificant for the CMP, moderate for the RMP and highest for the RMP + HA, resulting in a maximal downward traveling distance of 0 cm, 3-4 cm, and 9-10 cm, respectively. Correlation between the maximal traveling distance and zeta potential of the CMP, RMP, and RMP + HA confirmed surface charge as a dominant control on the MP mobility; while the increasing density of the MP, due to hetero-aggregation with soil minerals, was identified as a driving mechanism for its downward transport, despite its intrinsic density lower than water. Occurrence of only the lower-sized rod-shaped plastic fibers at the maximal traveling distance suggested the natural aging, a process leading to plastic vibration and fragmentation, was conducive to plastic translocation. The three explored classes of antibiotic resistance genes (ARGs) (tetracycline, beta-lactam and sulfonamide) were all detected in the plastic surface, suggesting the MP may function as a potential pathway for the dissemination of ARGs to the deeper soil layer. These findings are important to understand the concentration distribution of both the MPs and ARGs in agriculture impacted soils, a natural reservoir of both emerging contaminants.

There are challenges involved in the synergistic dissipation of antibiotics and antibiotic resistance genes (ARGs) in soil because ARGs are affected by not only the selective pressure of antibiotics but also microbial community succession and co-existing pollutants. Here, magnetic biochars (MBCs) at various magnetic iron-to-biochar mass ratios (3:1, 2:1, 1:1, 1:2, 1:3, 1:5, and 1:7) were synthesized to develop a strategy for the synergistic dissipation of oxytetracycline (OTC) and its resistance gene (tet) in soils with and without polybutylene adipate terephthalate (PBAT) microplastics (MPs). The results showed that MBC12 (1:2) achieved the greatest dissipation efficiencies of OTC in soils without and with PBAT MPs (95.27% and 94.50%, respectively). The reductive degradation of OTC via promoting the electron transfer during conversion between Fe(III) and Fe(II) overwhelmed biodegradation of OTC. MBCs effectively hindered the spread of tet in soil without PBAT MPs, with the efficiencies more than 60%; but they had little influence on its spread in soil with PBAT MPs, excluding MBC15 (1:5). The absolute abundance of tet, regardless of PBAT MPs, just significantly positively correlated with Serratia (the added exogenous tet-host bacterium), indicating that MBCs inhibited the horizontal transfer of tet at the inter-genus level. Down-regulating the degradation/utilization/assimilation metabolic function by MBCs (excluding MBC31, 3:1) contributed to the hindering class 1 integron gene (intI1)-driven tet propagation. After considering efficiency, cost and toxic effects, MBC12 (1:2) was recommended to use for synergistic dissipation of OTC and tet in soils without and with PBAT MPs.

Whether and how conventional (CP) and biodegradable microplastics (BP) affect viral communities and virus-carried antibiotic resistance genes (ARGs) in agricultural soils remains largely unknown. Here, we established a soil microcosm incubation with addition of 1 % (w/w) microplastics (MPs) in maize-cultivated soil that had been treated with different fertilizers for over 10 years, and the dynamic variations of viral communities and ARG profiles were investigated using a combination of metagenomic and metatranscriptomic methods. Our results revealed that BP, but not CP, significantly decreased viral α-diversity, changed viral community structure, community resistance and taxonomic turnover in all fertilized treatments. Caudoviricetes was the most dominate viral class and BP significantly increased the abundances of viral families (i.e. Phycodnaviridae) in all fertilized treatments, while CP altered the viral family abundance mainly observed in manure-amended soils. Also, BP was associated with increased ARG α-diversity, altered ARG community structure and community resistance, especially at the transcriptional level. Particularly, BP significantly enriched high-risk ARGs and mobile genetic elements (MGEs) in soils regardless of fertilization regimes. Correlation analysis revealed the important role of lytic viruses in shaping the abundance of high-risk ARGs and MGEs. Furthermore, BP induced more variations in reconstructed metagenome-assembled genome (MAGs), and significantly enriched high-risk ARGs carried by phage genomes. Co-occurrence patterns revealed three Actinobacteriota MAGs as primary viral hosts sharing high-risk ARGs with phages and containing multiple MGEs. Notably, we identified four viral genomes carrying ARG transcripts identical to their hosts. Both CP and BP differentially stimulated ARG expression in these virus-host systems, withmarkedlystronger effects observed in manure-amended soils. In conclusion, this study revealed a high risk of ARG dissemination induced by biodegradable MP residues regardless of fertilization regimes, while conventional MPs strengthen the ARG health risks mainly in manure-amended soils.

Microplastics (MPs) and antibiotic resistance genes (ARGs) are emerging contaminants that have garnered significant attention due to their prevalence in soil. Although many studies have already highlighted the effects of MPs on soil microbial communities and ARGs spread, their differential variation in both habitats (plastisphere and surrounding soil solution) and the effect of aging degree of MPs has not been clarified. Herein, we conducted a microcosm experiment to investigate the effects of aged-treated MPs on microbiome and antibiotic resistome of the plastisphere and the surrounding soil solution. The results showed that MPs with different aging degree altered bacterial community compositions. The plastisphere was enriched more unique bacterial species compared to its surrounding solution, particularly for 7d-aged MPs. MPs aging promoted certain ARGs dissemination, which depends on habitats, ARGs types and their aging degree. MPs always promoted the enrichment of Proteobacteria as the top host, especially aged MPs, which explained the enhanced ARGs dissemination after aged MPs addition. The primary hosts of most ARGs shifted from surrounding soil solution to the plastisphere. In addition to these individual host species, population hosts, including key taxa within co-occurrence network modules and functional bacterial populations, also contributed to ARGs dissemination. Unique bacteria from the plastisphere were included in network key modules and promoted ARGs dissemination, but not in the solution. Bacterial functions and pathways both played pivotal roles in ARGs dissemination. Interestingly, the influence of these population-level hosts, along with associated bacterial functions and metabolic pathways, on ARG spread was more pronounced in the surrounding soil solution than in the plastisphere. According to variance partitioning analysis, horizontal gene transfer via MGEs plays an important role in ARGs dissemination with 54-78% contribution in two habitats. Overall, these findings provide the differential processes and driving mechanisms of ARGs dissemination between the plastisphere and surrounding soil solution.

No abstract available

In this study, oversized microplastics (OMPs) were intentionally introduced into soil containing manure-borne doxycycline (DOX). This strategic approach was used to systematically examine the effects of combined OMP and DOX pollution on the growth of pak choi, analyze alterations in soil environmental metabolites, and explore the potential migration of antibiotic resistance genes (ARGs). The results revealed a more pronounced impact of DOX than of OMPs. Slender-fiber OMPs (SF OMPs) had a more substantial influence on the growth of pak choi than did coarse-fiber OMPs (CF OMPs). Conversely, CF OMPs had a more significant effect on the migration of ARGs within the system. When DOX was combined with OMPs, the negative effects of DOX on pak choi growth were mitigated through the synthesis of indole through the adjustment of carbon metabolism and amino acid metabolism in pak choi roots. In this process, Pseudohongiellaceae and Xanthomonadaceae were key bacteria. During the migration of ARGs, the potential host bacterium Limnobacter should be considered. Additionally, the majority of potential host bacteria in the pak choi endophytic environment were associated with tetG. This study provides insights into the intricate interplay among DOX, OMPs, ARGs, plant growth, soil metabolism, and the microbiome.

Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).

The growing population and associated increase in municipal solid waste (MSW) have promoted the use of sustainable waste management strategies. Given its high organic content, MSW can be treated through anaerobic digestion (AD) and aerobic composting (AC) to recover value-added products such as bioenergy and soil amendments. However, MSW is also recognized as a relevant source of antibiotic resistance genes (ARGs), raising concerns about environmental and public health impacts. This study aimed to elucidate the dynamics of ARGs and antibiotic compounds during the treatment of the organic fraction of municipal solid waste (OFMSW) through an integrated AD–AC system. By combining metagenomics and untargeted metabolomics, a comprehensive characterization of shifts in the microbial community, ARGs, and antibiotic compounds throughout the treatment stages was achieved. Shotgun sequencing enabled an in-depth resistome analysis based on metagenome-assembled genomes (MAGs), while untargeted metabolomics revealed the occurrence and transformation of antibiotic compounds across the system. The integrated process resulted in a significant differentiation of microbial communities, resistome, and antibiotic compounds profiles, at different stages of the waste treatment plant. AD samples were mostly dominated by aminoglycoside and lincosamide ARGs, whereas AC samples by macrolide and rifamycin ARGs. Despite differences in drug class dominance, the composting process significantly increased both the ARGs diversity (i.e., digestate: H = 2.6 ± 0.1; mature compost: H = 3.7 ± 0.1) and abundance (i.e., mature compost vs. digestate: log2(FC) = 3.7). Untargeted metabolomics revealed distinct distributions of antibiotics among the six matrices (i.e., pulp, digestate, solid fraction, liquid fraction, fresh compost, and mature compost) suggesting limited degradation or transformation of some classes during treatment. Digestate was enriched in phenazines and trimethoprim derivatives, whereas mature compost mainly included phenicols and sulfonamides. This study provides valuable insights into the fate of antibiotic resistance genes and the persistence of antibiotic compounds in an integrated AD and AC system treating OFMSW. Moreover, it was shown how the integration of -omics techniques as metagenomics and metabolomics can be systematically utilized to detect emerging ARGs and antibiotic compounds dynamics and monitor their ongoing evolution in biological waste treatment plants.

Microplastics (MPs) are increasingly recognized as hotspots for antibiotic resistance genes (ARGs), yet the combined effects of polymer type and particle size on ARG dynamics in the soil plastisphere remain unclear. Here, we employed metagenomic assembly and binning to explore how MP polymer type and particle size jointly modulate ARG carrying frequencies (ACFs), mobility, and microbial hosts with polyethylene (PE), polystyrene (PS), and biodegradable polybutylene succinate (PBS) MPs across a size gradient (1000, 500, and 106 μm). PBS, PS, and PE plastispheres exhibited different size-related trends in ARG association, with PBS showing the strongest and most consistent decline in ACFs. Only PBS showed a corresponding reduction in ARG-MGE co-localization, suggesting size-dependent constraints on horizontal gene transfer. Distinct ARG combinations in ARG-Carrying Contigs (ACCs) also showed plastic-type selectivity, with complex resistance clusters absent in 106 μm PBS samples, potentially due to environmental constraints that limit the assembly or persistence of multigene resistance structures. Potential pathogens Enterobacter bugandensis and Stutzerimonas urumqiensis were markedly reduced in 106 μm PBS samples, a pattern not observed in PS or PE. Bacterial community analysis revealed that smaller PBS particles were associated with reduced richness, increased evenness, and more competitive interactions within co-occurrence networks. These features, together with the decline in ARG abundance and mobility, suggest that enhanced ecological filtering may occur in smaller biodegradable plastispheres, jointly limiting the persistence of resistance genes and their bacterial hosts. Together, our findings highlight the importance of considering both MP type and particle size in assessing plastisphere-associated ARG risks.

As a novel agricultural practice, the reuse of food waste compost and digestate as fertilizers leads to a circular economy, but inevitably introduces bio-contaminants such as antibiotic resistance genes (ARGs) into the agroecosystem. Moreover, heavy metal and antibiotic contamination in farmland soil may exert selective pressures on the evolution of ARGs, posing threats to human health. This study investigated the fate, influencing mechanisms and potential risks of ARGs in a soil-vegetable system under different food waste fertilization and remediation treatments and soil contamination conditions. Application of food waste fertilizers significantly promoted the pakchoi growth, but resulted in the spread of ARGs from fertilizers to pakchoi. A total of 56, 80, 84, 41, and 73 ARGs, mobile genetic elements (MGEs) and metal resistance genes (MRGs) were detected in the rhizosphere soil (RS), bulk soil (BS), control soil (CS), root endophytes (RE), and leaf endophytes (LE), respectively. Notably, 7 genes were shared in the above five subgroups, indicating a specific soil-root-endophytes transmission pathway. 36 genes were uniquely detected in the LE, which may originate from airborne ARGs. The combined application of biochar and fertilizers reduced the occurrence of ARGs and MGEs to some extent, showing the remediation effect of biochar. The average abundance of ARGs in the RS, BS and CS was 3.15 × 10-2, 1.31 × 10-2 and 2.35 × 10-1, respectively. Rhizosphere effects may reduce the abundance of ARGs in soil. The distribution pattern of ARGs was influenced by the types of soil, endophyte and contaminant. MGEs are the key driver shaping ARGs dynamics. Soil properties and pakchoi growth status may affect the bacterial composition, and consequently regulate ARGs fate, while endophytic ARGs were more impacted by biotic factors. Moreover, the average daily doses of ARGs from pakchoi consumption is 107-109 copies/d/kg, and its potential health risks should be emphasized.

No abstract available

The reuse of organic waste streams, such as composted sewage sludge (CSS), provides agronomic benefits, but also represents a critical pathway for the environmental dissemination of antibiotic resistance genes (ARGs). The consequences of CSS application for soil resistome dynamics and microbial ecology remain insufficiently understood. Here, we investigated paddy soils in Tsuruoka, Japan, under three fertilization treatments: CSS, chemical fertilizer (CF), and their combination (CSS + CF). Quantitative PCR targeted total bacterial (16S rRNA), fecal indicators (E. coli, Enterococcus spp.), mobile genetic element (MGE) (inlt1), and five ARGs (sul1, blaTEM, blaCTX-M Groups 1, 2, and 9). CSS amended soils showed elevated levels of intI1, sul1, and blaTEM in 2023, with blaTEM persisting into 2024. Although both E. coli and Enterococcus spp. showed weak correlations with ARGs, only Enterococcus spp. (ρ = 0.37, p < 0.05) showed statistically significant associations with intI1. Network analysis demonstrated that CSS fostered a highly interconnected resistome with sul1 emerging as a central hub linking multiple bacterial families. In contrast, CF maintained a sparse modular structure while CSS + CF generated an intermediate network. Collectively, these results demonstrate that CSS amplifies the potential for ARG dissemination by fostering a highly connected resistome, whereas co-application with chemical fertilizers partially disrupts this connectivity, thereby reducing dissemination risk in the soil environment. Our findings provide field-based evidence of the environmental impacts of waste-derived fertilization and underscore the need for integrated fertilization strategies and ARG surveillance to promote sustainable soil management and safeguard environmental health.

The widespread use of antibiotics, combined with pervasive exposure to diverse environmental media, has intensified the global challenge of antibiotic resistance. Accumulating evidence reveals that beyond direct antibiotic pressure, residual non-antibiotic chemicals—despite lacking intrinsic antibacterial activity—can significantly promote the enrichment and spread of antibiotic resistance genes (ARGs) in farmland soils through indirect mechanisms such as inducing oxidative stress, altering microbial community structure, and enhancing both vertical and horizontal gene transfer. To address this issue, the present study investigates the influence of representative non-antibiotic contaminants commonly detected in agricultural environments—including pesticides (e.g., Omethoate, imidacloprid, and atrazine), industrial pollutants (e.g., PCB138, BDE47, benzo [a] pyrene, 2,3,7,8-tetrachlorodibenzo-p-dioxin [TCDD], and benzene), plastic-associated compounds (e.g., Polyethylene trimer, phthalates, and tributyl acetylcitrate), and ingredients from personal care products (e.g., triclosan and bisphenol A)—on ARG transmission dynamics. Leveraging bioinformatics resources such as the CARD database, PDB, AlphaFold, and molecular sequence analysis tools, we identified relevant small-molecule ligands and macromolecular receptors to construct a simulation system modeling ARG transfer pathways. Molecular docking and molecular dynamics (MD) simulations were then implemented, guided by a Plackett–Burman experimental design, to systematically evaluate the impact of individual and co-occurring pollutants. The resulting data were processed using advanced analytical tools, and MD trajectories were interpreted at the molecular level across three scenarios: an unperturbed (blank) system, single-pollutant exposures, and dual-pollutant combinations. By integrating computational simulations with machine learning approaches, this work uncovers the “co-selection” effect exerted by non-antibiotic chemical residues in shaping the environmental resistome, thereby providing a mechanistic and scientific basis for comprehensive risk assessment of agricultural non-point source pollution and the development of effective soil health management and antimicrobial resistance containment strategies.

Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management to fertilization for plant biomass production, and it is known as fertirrigation. Here we evaluate public datasets of soil metagenomes mining for changes in antibiotic resistance genes (ARGs) of soils from sugarcane mesocosms repeatedly amended with vinasse. The metagenomes were annotated using the ResFam database. We found that the abundance of open read frames (ORFs) annotated as ARGs changed significantly across 43 different families (p-value < 0.05). Co-occurrence network analysis revealed distinct patterns of interactions among ARGs, suggesting that nutrient amendment to soil microbial communities can impact on the coevolutionary dynamics of indigenous ARGs within soil resistome.

Saprophagous fauna like the oriental edible beetle (P. brevitarsis) plays a fundamental role in converting organic wastes into biofertilizer. Accumulating evidence has shown that soil fauna can reduce the abundance of ARGs, although the underlying mechanism of ARG reduction is still unclear. ABSTRACT Livestock wastes contain high levels of antibiotic resistance genes (ARGs) and a variety of human-related pathogens. Bioconversion of livestock manure using larvae of the beetle Protaetia brevitarsis is an effective technique for waste reduction and value creation; however, the fate of manure ARGs during gut passage and interaction with the gut microbiome of P. brevitarsis remains unclear. To investigate this, we fed P. brevitarsis with dry chicken manure for 6 days and measured bacterial community dynamics and ARG abundance and diversity along the P. brevitarsis gut tract using high-throughput quantitative PCR and metagenomics approaches. The diversity of ARGs was significantly lower in larval midgut, hindgut, and frass than in raw chicken manure, and around 80% of pathogenicity-related genes (PRGs) exhibited reduced abundance. Network analysis demonstrated that Bacteroidetes and Firmicutes were the key bacterial phyla associated with ARG reduction. Metagenomic analysis further indicated that ARGs, mobile genetic elements (MGEs), and PRGs were simultaneously attenuated in the hindgut, implicating a decreased likelihood for horizontal gene transfer (HGT) of ARGs among bacteria and pathogens during manure bioconversion. Our findings demonstrated that the attenuation of ARGs is strongly associated with the variation of the gut microbiome of P. brevitarsis, providing insights into mechanisms of risk mitigation of ARG dissemination during manure bioconversion. IMPORTANCE Saprophagous fauna like the oriental edible beetle (P. brevitarsis) plays a fundamental role in converting organic wastes into biofertilizer. Accumulating evidence has shown that soil fauna can reduce the abundance of ARGs, although the underlying mechanism of ARG reduction is still unclear. In our previous research, we found a large reduction of ARGs in vegetable roots and leaves from frass compared with raw manure, providing a promising biofertilizer for soil-vegetable systems. Therefore, in this study, temporal dynamic changes in the microbiomes of the donor (chicken manure) and host (P. brevitarsis) were investigated, and we found a close association between the gut microbiome and the alteration of ARGs. These results shed new light on how the insect gut microbiome can mitigate manure-borne ARGs and provide insights into the bioconversion process via a typical member of the saprophagous fauna, P. brevitarsis.

Penicillin fermentation dreg (PFD) is a solid waste discharged by pharmaceutical enterprises in the fermentation production process. Due to the residual antibiotic of PFD, the risk of antibiotic resistance bacteria (ARB) generation should be considered in the disposal process. High-throughput quantitative PCR (HT-qPCR) and 16S rRNA gene sequencing were performed to investigate the effect of PFD on the dynamics of antibiotic resistance genes (ARGs) and bacterial community during a lab-scale soil experiment. After the application of PFD, the bacterial number and diversity showed an obvious decrease in the initial days. The abundances of Streptomyces and Bacillus, which are the most widespread predicted source phyla of ARGs, increased remarkably from 4.42% to 2.59%-22.97% and 21.35%. The increase of ARGs was observed during the PFD application and the ARGs carried by PFD itself contributed to the initiation of soil ARGs. The results of redundancy analysis (RDA) show that the shift in bacterial community induced by variation of penicillin content is the primary driver shaping ARGs compositions.

Antibiotic resistance genes (ARGs) are considered environmental pollutants posing a potential human health risk. Silage is an important and traditional feed, mainly for ruminants. ABSTRACT Antibiotic resistance genes (ARGs) are recognized as contaminants due to their potential risk for human and environment. The aim of the present study is to investigate the effects of pyroligneous acid (PA), a waste of biochar production, on fermentation characteristics, diversity, and dynamics of ARGs during ensiling of alfalfa using metagenomic analysis. The results indicated that PA decreased (P < 0.05) dry matter loss, pH value, gas production, coliform bacteria count, protease activity, and nonprotein-N, ammonia-N, and butyric acid contents and increased (P < 0.05) lactic acid content during ensiling. During fermentation, Bacteria, Firmicutes, and Lactobacillus were the most abundant at kingdom, phylum, and genus levels, respectively. Pyroligneous acid reduced the relative abundance of Bacteria and Firmicutes and increased that of Lactobacillus. The detected ARGs belonged to 36 drug classes, including mainly macrolides, tetracycline, lincosamides, and phenicol. These types of ARGs decreased during fermentation and were further reduced by PA. These types of ARGs were positively correlated (P < 0.05) with fermentation parameters like pH value and ammonia-N content and with bacterial communities. At the genus level, the top several drug classes, including macrolide, tetracycline, lincosamide, phenicol, oxazolidinone, streptogramin, pleuromutilin, and glycopeptide, were positively correlated with Staphylococcus, Streptococcus, Listeria, Bacillus, Klebsiella, Clostridium, and Enterobacter, the potential hosts of ARGs. Overall, ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community composition. Ensiling could be a feasible way to mitigate ARGs in forages. The addition of PA could not only improve fermentation quality but also reduce ARG pollution of alfalfa silage. IMPORTANCE Antibiotic resistance genes (ARGs) are considered environmental pollutants posing a potential human health risk. Silage is an important and traditional feed, mainly for ruminants. ARGs in silages might influence the diversity and distribution of ARGs in animal intestinal and feces and then the manure and the manured soil. However, the diversity and dynamics of ARGs in silage during fermentation are still unknown. We ensiled alfalfa, one of the most widely used forages, with or without pyroligneous acid (PA), which was proved to have the ability to reduce ARGs in soils. The results showed that ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community. The majority of ARGs in alfalfa silage reduced during fermentation. The addition of PA could improve silage quality and reduce ARG pollution in alfalfa silage. This study can provide useful information for understanding and controlling ARG pollution in animal production.

Plastic pollution is one of the most resilient types of pollution and is considered a global environmental threat, particularly in the marine environment. This study aimed to identify plastic-degrading bacteria from the plastisphere and their pharmaceutical and therapeutic potential. We collected samples from soil and aquatic plastisphere to identify the bacterial communities using shotgun metagenomic sequencing and bioinformatic tools. Results showed that the microbiome comprised 93% bacteria, 0.29% archaea, and 3.87% unidentified microbes. Of these 93% of bacteria, 54% were Proteobacteria , 23.9% were Firmicutes , 13% were Actinobacteria , and 2.1% were other phyla. We found that the plastisphere microbiome was involved in degrading synthetic and polyhydroxy alkanoate (PHA) plastic, biosurfactant production, and can thrive under high temperatures. However, no association existed between thermophiles, synthetic plastic or PHA degraders, and biosurfactant-producing bacterial species except for Pseudomonas . Other plastisphere inhabiting plastic degrading microbes include Streptomyces, Bacillus, Achromobacter, Azospirillum, Bacillus, Brevundimonas, Clostridium, Paenibacillus, Rhodococcus, Serratia, Staphylococcus, Thermobifida, and Thermomonospora. However, the plastisphere microbiome showed potential for producing secondary metabolites that were found to act as anticancer, antitumor, anti-inflammatory, antimicrobial, and enzyme stabilizers. These results revealed that the plastisphere microbiome upholds clinical and environmental significance as it can open future portals in a multi-directional way.

Introduction Dairy cattle waste is a globally significant source of organic fertilizer which contains a cocktail of microbes and antibiotic resistance genes (ARGs). These ARGs may present a risk to human and animal health, yet there is still limited farm-system-level understanding of how long-term and multiple slurry applications alter field soil resistomes and total microbial communities. Methods Using metagenomics, we assessed both immediate and longer-term changes in grassland field soil resistomes and bacterial communities over a year of routine cattle slurry application. Results Our findings suggest that soil microbial communities are resilient to bacteria and ARGs introduced via slurry, even after repeated applications. Most slurry-borne ARGs were not enriched in field soil, however, those common in soil, such as rifamycin resistance genes, were consistently elevated relative to field soil with no history of slurry application. We observed transient increases in slurry-associated macrolide-lincosamide-streptogramin ARGs, however, their persistence appeared to be influenced by timing of slurry application. Similar transient effects were shown by the recovery of a high quality, slurry-associated Proteiniphilum spp. metagenome assembled genome (MAG). Discussion We show that MAGs represent a powerful tool for examining the transfer of slurry-borne microorganisms, as they can be more characteristic of these environments than typical sentinel organisms which are easily cultivated. Our findings indicate that while the soil bacterial community shows considerable resilience to slurry-borne bacteria and ARGs, this may be diminished by temporal factors that remain largely unexplored and poorly understood. This is important because resilience inferred from short-term observations may not fully capture delayed or transient responses, potentially leading to underestimation of the persistence of slurry-borne bacteria and ARGs.

Virulence factor genes (VFGs) pose a potential threat to ecological security and animal health, and have attracted increasing attention in the livestock industry. As one of the primary livestock types, dairy cattle may be an important source of VFG transmission. However, the distribution, transmission, and evolution of VFGs in the gastrointestinal tract and surrounding environment of dairy cattle remain unclear. In the present study, a total of 263 samples were collected from cows, calves, colostrum, farm wastewater, and soil. Metagenomics was conducted to analyze changes in the microbiome and VFGs characteristics in these ecological niches. The VFGs of the cows showed distinct differences between the rumen and feces, and were influenced by the region. The dominant VFG hosts was regulated by their microbial structure. Colostrum administration of cows increased VFG abundance in their newborn calf feces sharply and Enterobacteriaceae became the primary host. While diet was the primary driving force for the temporal variation in calf VFGs. For samples of the surrounding environment, water and soil had higher VFG concentrations and were more structurally stable. Moreover, extensive interactions between the mobile genetic elements and VFGs and gene mobile analysis map based on metagenomic binning both displayed the potential horizontal transfer ability of VFGs in the cows and environment. Our study revealed the prevalence, diffusion, and regulatory factors of VFGs in dairy cattle production systems, providing novel insights into reducing livestock VFGs and limiting their spread.

The plastisphere may act as reservoir of antibiotic resistome, accelerating global antimicrobial resistance dissemination. However, the environmental risks in the plastisphere of field microplastics (MPs) in farmland remain largely unknown. Here, antibiotic resistance genes (ARGs) and virulence factors (VFs) on polyethylene microplastics (PE-MPs) and polybutylene adipate terephthalate and polylactic acid microplastics (PBAT/PLA-MPs) from residues were investigated using metagenomic analysis. The results suggested that the profiles of ARG and VF in the plastisphere of PBAT/PLA-MPs had greater number of detected genes with statistically higher values of diversity and abundance than soil and PE-MP. Procrustes analysis indicated a good fitting correlation between ARG/VF profiles and bacterial community composition. Actinobacteria was the major host for tetracycline and glycopeptide resistance genes in the soil and PE-MP plastisphere, whereas the primary host for multidrug resistance genes changed to Proteobacteria in PBAT/PLA-MP plastisphere. Besides, three human pathogens, Sphingomonas paucimobilis, Lactobacillus plantarum and Pseudomonas aeruginosa were identified in the plastisphere. The PE-MP plastisphere exhibited a higher transfer potential of ARGs than PBAT/PLA-MP plastisphere. This work enhances our knowledge of potential environmental risks posed by microplastic in farmland and provides valuable insights for risk assessment and management of agricultural mulching applications.

Plastic pollution is a growing environmental concern, particularly in agricultural soils where plastics are widely used. Biodegradable plastics such as polybutylene succinate (PBS) and polybutylene adipate-co-terephthalate (PBAT) are increasingly promoted as sustainable alternatives, yet their environmental fate under changing climate and land-use conditions remains poorly understood. This study investigated the plastisphere microbiome associated with PBS, PBAT, and polyethylene (PE) as a reference, under conventional and organic farming systems and both ambient and simulated future climate scenarios. We assessed microbial colonization, plastic degradation, and bacterial-fungal interactions over one year of soil exposure. Agricultural practices significantly influenced the PBS plastisphere microbiome and PBAT bacterial richness, while climate effects were minor and limited to specific time points. No treatment significantly affected the molar mass loss of biodegradable plastics, although PBS degraded faster than PBAT. Microbial community composition shifted over time, with bacterial and fungal richness peaking at 160 or 270 days, and gene copy numbers highest at 60 or 365 days. Early colonization was dominated by a few genera, including Sphingomonas, Hymenobacter, Massilia, Vishniacozyma, Alternaria, and Mycosphaerella, many of which are known plastic colonizers and potential degraders. Co-occurrence networks revealed positive associations between dominant bacterial and fungal taxa. These findings provide new insights into the temporal dynamics and environmental drivers of plastisphere microbiomes in agricultural soils. Understanding microbial succession and interactions on biodegradable plastics is essential for assessing their degradation potential and environmental risks, particularly regarding microplastic formation and the persistence of plastic residues in terrestrial ecosystems.

A mesocosm experiment was set-up to investigate the effects of low-density polyethylene (LDPE) fragments deriving from plastic film on soil ecology, rhizosphere and plant (Salvia officinalis L.) fitness. The internal transcribed spacer (ITS) and 16S metagenomic analysis was adopted to evaluate taxonomic and functional shifts of both soil and rhizosphere under the influence of microplastics (MPs). Photosynthetic parameters and enzymes involved in oxidative stress were assessed to unveil the plant physiological state. MP fragments were analysed by scanning electron microscope (SEM) and metagenomics to investigate the plastisphere. Microbial biomarkers of MPs pollution were identified in soil and rhizosphere, reinforcing the concept of molecular biomonitoring. Overall, Bacillus, Nocardioides and Streptomyces genera are bacterial biomarkers of MPs pollution in soil whereas Aspergillus, Fusarium and Trichoderma genera, and Nectriaceae family are fungal biomarkers of MPs polluted soil. The data show that the presence of MPs promotes the abundance of taxa involved in the soil N cycle, but simultaneously reduces the endophytic interaction capability and enhances pathogen related functions at the rhizosphere level. A significant decrease in chlorophyll levels and increase of oxidative stress enzymes was observed in plants grown in MPs-polluted soil. The SEM observations of MPs fragments revealed a complex colonisation, where bacteria (Bacillus in MPSo and Microvirga in MPRz) and fungi (Aspergillus in MPSo and Trichoderma in MPRz) represent the main colonisers. The results demonstrate that the presence of MPs causes changes in the soil and rhizosphere microbial community and functions leading to negative effects on plant fitness.

Microplastics are recognized as environmental vectors for antibiotic resistance genes (ARGs), a role traditionally ascribed to physical mechanisms such as biofilm-enhanced horizontal gene transfer. Here, we uncover a chemistry-driven pathway that fundamentally surpasses the traditional passive vector model. We show that π‑conjugated polystyrene (PS) microplastics serve as powerful chemical hazard amplifyers by specifically concentrating the signaling molecule indole on their surfaces through π-π stacking and electrostatic interactions (binding energy = -128.56 kcal/mol), creating localized interfacial risk hotspots. These hotspots drive the reprogramming of soil microbiomes, as evidenced by distinct transformations in dissolved organic matter (DOM), and promote a cross-kingdom microbial alliance centered on the keystone fungus Pseudeurotium. This fungal hub transmits the amplified indole signal to bacterial degraders, markedly elevating the dissemination risk of clinically relevant ARGs (e.g., sul2). Through an integration of molecular simulations, multi-omics analyses, and causal modeling, our structural equation modeling (SEM) identifies the amplified indole signal as the primary direct driver of ARG abundance (path coefficient β = 0.47)-an effect 23.5 times greater than that of the PS polymer itself. Our findings establish "Chemical Interfacial-Driven Network Engineering (CIDNE)" as a pivotal mechanism, redefining how synthetic materials actively reshape microbial networks and escalate environmental resistome risk through molecular-scale interfacial interactions.

Antibiotic resistance genes (ARGs) and microplastics (MPs) are recognized as emerging contaminants and threats to global human health. Despite both of them being significantly detected in their "hotspots", i.e., waste activated sludge (WAS), rare studies on how MPs affect ARGs and antibiotic-resistant bacteria (ARB) in anaerobic sludge digestion are available. Herein, the fate of ARGs and ARB after exposure to MPs of three dosages (10, 30, and 80 particles/g-TS), three polymer types (LDPE, PET, and PS), and three branching extents (LDPE, LLDPE, and HDPE) in anaerobic sludge digestion was investigated. Metagenomic results indicated that all variants of MPs resulted in an increase of the relative abundance of ARGs in the digester compared to the control. The abundance of ARGs demonstrated a dosage-dependent relationship within the range from 10 to 80 particles/g-TS, resulting in an increase from 4.5 to 27.9% compared to the control. Branching structure and polymer type influence ARG level in the sludge digester as well. Mechanism studies revealed that LDPE selectively enriched potential ARB and ARGs in the surface biofilm, possibly creating a favorable environment for ARB proliferation and ARG exchange. Furthermore, vertical transfer of ARGs was facilitated by LDPE through increasing bacterial cell proliferation accompanied by the enhancement of relevant functional genes. The elevated abundance of mobile genetic elements (MGEs) and ARGs-carrying plasmids also demonstrated that MGE-mediated horizontal transfer was promoted by LDPE at 80 particles/g-TS. This effect was compounded by increased oxidative stress, cell membrane permeability, and cell cohesion, collectively facilitating horizontal ARG transfer. Consequently, both vertical and horizontal transfer of ARGs could be concurrently promoted by LDPE an in anaerobic sludge digester.

No abstract available

Plastic particles impact antibiotic resistance genes (ARGs) dissemination majorly via horizontal gene transfer (HGT) in environmental media, yet how different ARGs respond to plastic particles during HGT is rarely studied, and size-dependent effects of plastic particles on HGT remain debated. Here, we investigated polystyrene (PS) particles (20 nm, 80 nm, 2000 nm, 20000 nm) mediating HGT via transformation in Escherichia coli, using engineered pUC19-derived plasmids differing in size (3.75, 5.00, 7.50 kb) and replication capacity. Nanoplastics (NPs) enhanced transformation of 3.75 kb and 5.00 kb plasmids at 0.5 mg/L but inhibited transformation at 18, 36, and 72 mg/L, while consistently inhibiting that of 7.50 kb plasmids. Meanwhile, 2000-nm microplastics (MPs) monotonously promoted HGT efficiencies, yet 20000-nm MPs decreased them (0-72 mg/L). PS particle effects on HGT were independent of plasmid replication capacity. Enhancing mechanisms for HGT majorly involved increased membrane permeability via forming bacterial surface pores (NPs, 2000-nm MPs). The inhibiting mechanism stemmed from size-dependent physical barriers on cell membranes, as observed through scanning electron microscopy and laser scanning confocal microscopy. Three-dimensional models further simulated PS particle-induced spatial barriers on cell surfaces. Our findings improve understanding of environmental ARG dissemination driven by plastic pollution.

Microplastics (MPs) and antibiotic resistance genes (ARGs) are important pollutants in waste activated sludge (WAS), but their interactions during anaerobic digestion (AD) still need to be further explored. This study investigated variations in ARGs, mobile genetic elements (MGEs), and host bacteria during AD under the pressure of polyamide (PA), polyethylene (PE), and polypropylene (PP). The results showed that the MPs increased methane production by 11.7-35.5%, and decreased ARG abundance by 5.6-24.6%. Correlation analysis showed that the decrease of MGEs (plasmid, prophage, etc.) promoted the decrease of the abundance of multidrug, aminoglycoside and tetracycline resistance genes. Metagenomic annotation revealed that the reduction of key host bacteria (Arenimonas, Lautropia, etc.) reduced the abundance of major ARGs (rsmA, rpoB2, etc.). Moreover, PP MPs contributed to a reduction in the abundance of functional genes related to the production of reactive oxygen species, ATP synthesis, and cell membrane permeability, which was conducive to reducing the potential for horizontal gene transfer of ARGs. These findings provide insights into the treatment of organic waste containing MPs.

The impact of microplastic particles of micro- and nanometer sizes on microbial horizontal gene transfer (HGT) remains a controversial topic. Existing studies rely on traditional approaches, which analyze population behavior, leading to conflicting conclusions and a limited understanding. The present study addressed these limitations by employing a novel microfluidic chamber system for in situ visualization and precise quantification of the effects of different concentrations of polystyrene (PS) microbeads on microbial HGT at the single-cell level. The statistical analysis indicated no significant difference in the division times of both the donor and recipient bacteria across different PS microbead concentrations. However, as the concentration of PS microbeads increased from 0 to 2000 mg L-1, the average conjugation frequency of Escherichia coli decreased from 0.028 ± 0.015 to 0.004 ± 0.003. Our observations from the microfluidic experiments revealed that 500 nm PS microbeads created a barrier effect on bacterial conjugative transfer. The presence of microbeads resulted in reduced contact and interaction between the donor and recipient strains, thereby causing a decrease in the conjugation transfer frequency. These findings were validated by an individual-based modeling framework parameterized by the data from the individual-level microfluidic experiments. Overall, this study offers a fresh perspective and strategy for investigating the risks associated with the dissemination of antibiotic resistance genes related to microplastics.

Microplastic pollution is a rising environmental issue worldwide. Microplastics can provide a niche for the microbiome, especially for antibiotic-resistant bacteria, which could increase the transmission of antibiotic resistance genes (ARGs). However, the interactions between microplastics and ARGs are still indistinct in environmental settings. Microplastics were found to be significantly correlated with ARGs (p < 0.001), based on the analysis of samples taken from a chicken farm and its surrounding farmlands. Analysis of chicken feces revealed the highest abundance of microplastics (14.9 items/g) and ARGs (6.24 ×108 copies/g), suggesting that chicken farms could be the hotspot for the co-spread of microplastics and ARGs. Conjugative transfer experiments were performed to investigate the effects of microplastic exposure for different concentrations and sizes on the horizontal gene transfer (HGT) of ARGs between bacteria. Results showed that the microplastics significantly enhanced the bacterial conjugative transfer frequency by 1.4-1.7 folds indicating that microplastics could aggravate ARG dissemination in the environment. Potential mechanisms related to the up-regulation of rpoS, ompA, ompC, ompF, trbBp, traF, trfAp, traJ, and down-regulation of korA, korB, and trbA were induced by microplastics. These findings highlighted the co-occurrence of microplastics and ARGs in the agricultural environment and the exacerbation of ARGs' prevalence via rising the HGT derived from microplastics.

No abstract available