Carbendazim shapes microbiome and enhances resistome in the earthworm gut

Warming exacerbates the effects of pesticides on the soil collembolan gut microbiome and antibiotic resistome

In the context of global climate warming, studies have yet to fully clarify how pollutants affect the gut microbiome and antibiotic resistance genes (ARGs) in nontarget soil fauna. This study investigates the interactive effects of pesticide exposure (imidacloprid) and elevated temperature on the gut bacterial community and ARGs in the model soil collembolan Folsomia candida. Our results demonstrate warming exacerbates the toxicity of imidacloprid in collembolans. While exposure to both warming and pesticide significantly altered the gut microbial composition of F. candida, impairing microbial metabolic diversity and potential host defense mechanisms, it also increased collembolan mortality. This combined exposure significantly enhanced the abundance and diversity of ARGs in the collembolan gut. A notable correlation between ARGs and mobile genetic elements (MGEs) underscores the potential risk of ARG transmission. Co-occurrence network analysis identified 52 bacterial genera as potential ARG hosts. Additionally, pure-culture exposure experiments with the isolated bacterium Serratia liquefaciens revealed the adaptability of ARG hosts to pesticide and warming stress plays an important role in driving the observed increase in ARGs. In conclusion, this study highlights the synergistic effects of climate warming and pesticide contamination on nontarget soil organisms, emphasizing the potential long-term risks to soil ecosystem health and stability.

Co-exposure to cyazofamid and polymyxin E: Variations in microbial community and antibiotic resistance in the soil-animal-plant system

Human activity is accelerating the emergence of fungal pathogens, prompting substantial efforts to discover novel fungicides. Meanwhile, the runoff and spray drift from agricultural fields adversely affect aquatic and terrestrial nontarget organisms. However, few studies have examined the effects of co-contamination by agrochemical fungicides and pharmaceutical antibiotics on microorganisms and antibiotic resistance genes (ARGs) in the soil-animal-plant system. To further explore the mechanisms, an investigation was conducted into the individual and combined effects of a widely used fungicide (cyazofamid, CZF) and a last-resort antibiotic (colistin, polymyxin E, PME) in the soil-earthworm-tomato system. This study revealed that CZF and PME co-contamination exerted synergistic toxicity, significantly reducing earthworm survival and inhibiting tomato growth. This study found that the structure of microbial communities was more severely disturbed by the fungicide CZF than by the antibiotic PME, with the most severe impact being that of CZF + PME co-contamination. Fungicides and antibiotics had significantly distinct effects on bacterial functional pathways: CZF and CZF + PME treatments enhanced compound degradation, whereas PME treatments promoted biological nitrogen cycling. Moreover, co-contamination significantly increased the abundance of insertional and plasmid-associated genes and number of total ARGs in bulk and rhizosphere soil. In addition, the relationships between bacterial communities and the antibiotic resistome were investigated. The analysis revealed that Gram-positive bacteria (Sporosarcina, Bacillus, and Rhodococcus) capable of resistance and degradation, as well as the genes MexB (multidrug) and aadA2 (aminoglycoside) were enriched. Taken together, interactions between co-pollutants can significantly increase toxicity levels and the risk of ARG proliferation. The findings provide new insights into the potential impacts of co-contamination in complex real-life environments, such as soil-animal-plant systems.

Polyvinyl chloride microplastic triggers bidirectional transmission of antibiotic resistance genes in soil-earthworm systems

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.

Significant variations of bacterial communities among the developmental stages of Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae)

The yellow stemborer, Scirpophaga incertulas, is a monophagous pest of rice, attacking the crop from its vegetative to reproductive stages. Microorganisms are crucial in influencing the insect's life cycle, evolution, and ecology, presenting an avenue for understanding and improving management strategies. Present research employed advanced next-generation sequencing technology to investigate the microbiota of S. incertulas, a previously unexplored area for developmental stage associated microbial diversity. The study used 16 S rRNA V3-V4 region amplicon sequencing to determine the diversity of bacteria associated with different developmental stages of S. incertulas. Taxonomically, bacterial communities were classified into 25 phyla, encompassing 46 classes, 101 orders, 197 families, and 364 genera. The major phyla identified were Proteobacteria (39%), Firmicutes (39%), Actinobacteria (11%), and Bacteroidetes (7%), with Proteobacteria being the most predominant across all developmental stages except the larval stage, where Firmicutes took precedence. Moraxellaceae, Bacillaceae, Xanthomonadaceae, Sphingobacteriaceae, and Flavobacteriaceae were predominant families across all the developmental stages. However, in the egg and adult stages, the abundance of Bacillaceae was notably lower, whereas Prevotellaceae found significantly higher in adult stages. Dominant genera across all stages included Acinetobacter, Bacillus, Lactobacillus, Enterococcus, and Pseudomonas. The result showed that the highest number of Operational Taxonomic Units (OTUs) were in the larval stage (426 OTUs), the lowest in adults (251 OTUs), and the egg stage (254 OTUs). This suggests that the microbiota may play a role in the growth and development of S. incertulas. The predicted functional assessment of the associated S. incertulas microbiota revealed that the microbiota primarily participated in metabolic pathways, secondary metabolite biosynthesis, energy metabolism, signaling, and cellular processes. Our findings shed light on the significant variations in the microbial community and their predicted functions present in S. incertulas across developmental stages. The present study findings will help in developing novel microbiota-based management strategies.

Migration of fungicides, antibiotics and resistome in the soil-lettuce system

The emergence and spread of antibiotic resistance genes (ARGs) have become a serious issue in global agricultural production. However, understanding how these ARGs spread across different spatial scales, especially when exposed to both pesticides and antibiotics, has remained a challenge. Here, metagenomic assembly and binning methodologies were used to determine the spread pathway of ARGs in the soil-lettuce system under individual and combined exposure of fungicides (carbendazim and pyraclostrobin) and antibiotics (chlortetracycline and ciprofloxacin). These agrochemicals not only facilitated the spread of ARGs from soil to lettuce but also significantly elevated the risk of developing multi-antibiotic resistance among bacteria, especially to some antibiotic types (i.e. sulfonamide, aminoglycoside, quinolone, and tetracycline). ARGs could be migrated through distinct pathways, including both vertical and horizontal gene transfer, with plasmids playing a crucial role in facilitating the horizontal gene transfer. These transfer pathways have enabled key pathogenic bacteria belonging to the genera Acinetobacter, Pseudomonas, and Pantoea to acquire resistance and remain recalcitrant, posing the potential risk to crop health and food safety. In summary, our findings highlighted that fungicide and antibiotic could drive upward migration of ARGs in the soil-lettuce system and reduced the quality safety of agricultural products.

Development of multifunctional immobilized bacterial agents for multi-pesticides degradation and environment remediation

The proliferation of weeds, pests, and plant diseases in crop cultivation has driven the increased application of herbicide lactofen, insecticide acetamiprid, and fungicide carbendazim, contributing to environmental pollution. Microorganisms are requently employed to remove pesticide residues from the environment. However, Liquid bacterial agents encounter difficulties in transportation and preservation during application and the current immobilized bacterial agents have a single degradation function. This study developed immobilized bacterial agents containing the lactofen-degrading strain Bacillus sp. Za, the acetamiprid-degrading strain Pigmentiphaga sp. D-2, and the carbendazim-degrading strain Rhodococcus sp. djl-6. Preparation conditions, including activated carbon concentration, sodium alginate (SA), CaCl2, and immobilization time, were optimized using the response surface method (RSM). The degradation performance of the immobilized bacteria was evaluated, with degradation rates exceeding 70% for all three pesticides under conditions of 30 °C, pH 7.0, and 6% inoculation over 48 h. The immobilized bacterial agents were stored at pH 7.0 and 4 °C for 180 days, maintaining a preservation rate of 51.26% with a viable cell count of 1.04 × 108 CFU/g. These agents effectively remediated soil and water contaminated with multi-pesticides, achieving degradation rates of 92.50% and 98.50% for lactofen, 91.05% and 99.89% for acetamiprid, 88.43% and 98.99% for carbendazim within 21 in soil and 7 days in water, respectively. This study provides essential technical support for developing microbial agents capable of degrading multi-pesticides residues, with significant potential applications in agriculture and environmental protection.

Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails

BACKGROUND

Global warming is redrawing the map for invasive species, spotlighting the globally harmful giant African snail as a major ecological disruptor and public health threat. Known for harboring extensive antibiotic resistance genes (ARGs) and human pathogens, it remains uncertain whether global warming exacerbates these associated health risks.

METHODS

We use phenotype-based single-cell Raman with D2O labeling (Raman-D2O) and genotype-based metagenomic sequencing to investigate whether soil warming increases active antibiotic-resistant bacteria (ARBs) in the gut microbiome of giant African snails.

RESULTS

We show a significant increase in beta-lactam phenotypic resistance of active ARBs with rising soil temperatures, mirrored by a surge in beta-lactamase genes such as SHV, TEM, OCH, OKP, and LEN subtypes. Through a correlation analysis between the abundance of phenotypically active ARBs and genotypically ARG-carrying gut microbes, we identify species that contribute to the increased activity of antibiotic resistome under soil warming. Among 299 high-quality ARG-carrying metagenome-assembled genomes (MAGs), we further revealed that the soil warming enhances the abundance of "supercarriers" including human pathogens with multiple ARGs and virulence factors. Furthermore, we identified elevated biosynthetic gene clusters (BGCs) within these ARG-carrying MAGs, with a third encoding at least one BGC. This suggests a link between active ARBs and secondary metabolism, enhancing the environmental adaptability and competitive advantage of these organisms in warmer environments.

CONCLUSIONS

The study underscores the complex interactions between soil warming and antibiotic resistance in the gut microbiome of the giant African snail, highlighting a potential escalation in environmental health risks due to global warming. These findings emphasize the urgent need for integrated environmental and health strategies to manage the rising threat of antibiotic resistance in the context of global climate change. Video Abstract.

Effect of folpet on hypoglycaemia, intestinal microbiota, and drug resistance genes in mice

BACKGROUND

Folpet is a nonspecific sulfonamide fungicide widely used to protect crops from mildew. However, the in vivo effects of folpet on glucose metabolism homeostasis, gut microbiota, and abundance of drug resistance genes remain unknown. The purpose of this study was to assess the effects of the pesticide, folpet, on glucose metabolism homeostasis, and folpet-induced changes in the intestinal microbiota and resistance genes in mice.

METHODS

Mice were orally administered folpet at 0, 1, 10, and 100 mg/kg body weight/day for 5 weeks. Blood sugar levels in mice were measured after 5 weeks of folpet administration. Metagenomic sequencing and drug resistance gene analyses were performed to explore changes in the abundance of gut microbiota members and drug resistance genes in mice after folpet administration. Correlation analysis was performed using metabolomics to explore the relationship between intestinal microbiota, drug resistance genes, and glucose metabolism.

RESULTS

Mice in the folpet group had significantly lower blood glucose levels than those in the control group. The abundance of Atopobium, Libanicoccus, Collinsella, and Parabacteroides in the intestinal microbiota of folpet-treated mice was significantly higher than that in the control group. However, the abundance of Mailhella, Bilophila, Roseburia, and Bacteroides were reduced in folpet-treated mice. Compared with the control group, the abundance of APH6-Ic and AAC6-Ie-APH2-Ia resistance genes in mice treated with folpet significantly increased. The abundance of tetQ, ermE, and BahA resistance genes was significantly reduced after folpet treatment.

CONCLUSIONS

Folpet is associated with changes in the abundance of gut microbiota in mice and may also affect the abundance of drug-resistance genes and the regulation of blood glucose levels.

Biochar and theaflavins mitigate the antibiotic resistome and antibiotic-resistant pathogens in a soil-lettuce continuum

Antibiotic resistance can be transferred into the food chain, leading to increased risks to human health from ready-to-eat vegetables. Mitigating the transmission of antibiotic resistance from soil to vegetables by green materials is of great significance. Here, we deciphered the roles of biochar and theaflavins in mitigating antibiotic resistance genes (ARGs) and antibiotic-resistant pathogens (ARPs) in a soil-lettuce continuum. Metagenomic results showed that biochar led to a significant decrease in the abundance of ARGs in lettuce leaves, while theaflavins contributed to a significant reduction in the diversity and abundance of ARGs in soil, particularly targeting dominant ARG types such as sulfonamide and aminoglycoside resistance genes. Meanwhile, biochar and theaflavins alleviated the potential mobility of ARGs, in lettuce leaves and soil, respectively, including the spread of ARGs to human pathogens. In addition, the diversity of ARG hosts was reduced in the soil-lettuce continuum and ARPs were not detected in lettuce leaves after the application of biochar or theaflavins. Overall, this study provides a novel perspective on green materials for mitigating the antibiotic resistome and ARPs in the soil-lettuce continuum, contributing to food security and human health.

Metabolomics and microbiomics revealed the combined effects of different-sized polystyrene microplastics and imidacloprid on earthworm intestinal health and function

The coexistence of pesticides and plastic film residues in agricultural soils poses a significant threat to soil organisms due to their potential long-term contamination and combined toxic effects. Specifically, earthworms are at risk of simultaneously ingesting residual pesticides and microplastics, yet the impact of this combined exposure on their intestinal health and function remains poorly understood. In this study, earthworm (Eisenia fetida) were single and combined exposed to three particle sizes (10 μm, 500 μm, and 2 mm) of polyethylene microplastics (PE MPs) and imidacloprid (IMI) for 28 days, respectively. Our findings underscore that compared to single exposures, the combined exposure inflicted more profound injuries on intestinal tissues and elicited a heightened activation of intestinal digestive enzymes. Furthermore, the combined exposure significantly perturbed the relative abundance of several pivotal metabolic-associated gut microbiota, fostering an enrichment of pathogenic species. Metabolomics analysis showed combined exposure increased differential metabolites, disrupting amino acid, fatty acid, and carbohydrate metabolism in earthworm intestines, potentially hindering nutrient absorption and causing toxic metabolite accumulation. An integrated omics analysis implies that combined exposures have the potential to disrupt the relative abundance of crucial gut microbiota in earthworms, thereby altering their intestinal metabolism and subsequently impacting intestinal health and functionality. Overall, the results reveal that combined exposure of IMI and PE MPs exacerbate the negative effects on earthworm gut health, and this study holds significant implications for the holistic understanding of the combined toxic effects of microplastics and pesticide on soil ecosystems.

Gut microbiome and antibiotic resistance genes in plateau model animal (Ochotona curzoniae) exhibit a relative stability under cold stress

Antibiotic resistance genes (ARGs) carried by gut pathogens may pose a threat to the host and ecological environment. However, few studies focus on the effects of cold stress on intestinal bacteria and ARGs in plateau animals. Here, we used 16S rRNA gene sequencing and gene chip technique to explore the difference of gut microbes and ARGs in plateau pika under 4 °C and 25 °C. The results showed that tetracycline and aminoglycoside resistance genes were the dominant ARGs in pika intestine. Seven kinds of high-risk ARGs (aadA-01, aadA-02, ermB, floR, mphA-01, mphA-02, tetM-02) existed in pika's intestine, and cold had no significant effect on the composition and structure of pika's intestinal ARGs. The dominant phyla in pika intestine were Bacteroidetes and Firmicutes. Cold influenced 0.47 % of pika intestinal bacteria in OTU level, while most other bacteria had no significant change. The diversity and community assembly of intestinal bacteria in pika remained relatively stable under cold conditions, while low temperature decreased gut microbial network complexity. In addition, low temperature led to the enrichment of glycine biosynthesis and metabolism-related pathways. Moreover, the correlation analysis showed that eight opportunistic pathogens (such as Clostridium, Staphylococcus, Streptococcus, etc.) detected in pika intestine might be potential hosts of ARGs.

Comparative Analysis of Bacterial Community Structures in Earthworm Skin, Gut, and Habitat Soil across Typical Temperate Forests

Earthworms are essential components in temperate forest ecosystems, yet the patterns of change in earthworm-associated microbial communities across different temperate forests remain unclear. This study employed high-throughput sequencing technology to compare bacterial community composition and structure in three earthworm-associated microhabitats (skin, gut, and habitat soil) across three typical temperate forests in China, and investigated the influence of environmental factors on these differential patterns. The results indicate that: (1) From warm temperate forests to cold temperate forests, the soil pH of the habitat decreased significantly. In contrast, the physicochemical properties of earthworm skin mucus exhibited different trends compared to those of the habitat soil. (2) Alpha diversity analysis revealed a declining trend in Shannon indices across all three microhabitats. (3) Beta diversity analysis revealed that the transition from warm temperate deciduous broad-leaved forest to cold temperate coniferous forest exerted the most significant impact on the gut bacterial communities of earthworms, while its influence on the skin bacterial communities was comparatively less pronounced. (4) Actinobacteria and Proteobacteria were the predominant phyla in earthworm skin, gut, and habitat soil, but the trends in bacterial community composition differed among the three microhabitats. (5) Mantel tests revealed significant correlations between bacterial community structures and climatic factors, physicochemical properties of earthworm habitat soil, and physicochemical properties of earthworm skin mucus. The findings of this study offer novel perspectives on the interplay between earthworms, microorganisms, and the environment within forest ecosystems.

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale

Earthworms are critical in regulating soil processes and act as filters for antibiotic resistance genes (ARGs). Yet, the geographic patterns and main drivers of earthworm gut ARGs remain largely unknown. We collected 52 earthworm and soil samples from arable and forest ecosystems along a 3000 km transect across China, analyzing the diversity and abundance of ARGs using shotgun metagenomics. Earthworm guts harbored a lower diversity and abundance of ARGs compared to soil, resulting in a stronger distance-decay rate of ARGs in the gut. Greater deterministic assembly processes of ARGs were found in the gut than in soil. The earthworm gut had a lower frequency of co-occurrence patterns between ARGs and mobile genetic elements (MGEs) in forest than in arable systems. Viral diversity was higher in the gut compared to soil and was negatively correlated with bacterial diversity. Bacteria such as Streptomyces and Pseudomonas were potential hosts of both viruses and ARGs. Viruses had negative effects on the diversity and abundance of ARGs, likely due to the lysis on ARG-bearing bacteria. These findings provide new insights into the variations of ARGs in the earthworm gut and highlight the vital role of viruses in the regulation of ARGs in the soil ecosystem.

Assessing earthworm exposure to a multi-pharmaceutical mixture in soil: unveiling insights through LC-MS and MALDI-MS analyses, and impact of biochar on pharmaceutical bioavailability

In the European circular economy, agricultural practices introduce pharmaceutical (PhAC) residues into the terrestrial environment, posing a potential risk to earthworms. This study aimed to assess earthworm bioaccumulation factors (BAFs), the ecotoxicological effects of PhACs, the impact of biochar on PhAC bioavailability to earthworms, and their persistence in soil and investigate earthworm uptake mechanisms along with the spatial distribution of PhACs. Therefore, earthworms were exposed to contaminated soil for 21 days. The results revealed that BAFs ranged from 0.0216 to 0.329, with no significant ecotoxicological effects on earthworm weight or mortality (p > 0.05). Biochar significantly influenced the uptake of 14 PhACs on the first day (p < 0.05), with diminishing effects over time, and affected significantly the soil-degradation kinetics of 16 PhACs. Moreover, MALDI-MS analysis revealed that PhAC uptake occurs through both the dermal and oral pathways, as pharmaceuticals were distributed throughout the entire earthworm tissue without specific localization. In conclusion, this study suggests ineffective PhAC accumulation in earthworms, highlights the influence of biochar on PhAC degradation rates in soil, and suggests that uptake can occur through both earthworm skin and oral ingestion.

Combined toxicity of abamectin and carbendazim on enzymatic and transcriptional levels in the soil-earthworm microcosm

To reveal the toxicological mechanisms of pesticide mixtures on soil organisms, this study concentrated on evaluating enzymatic activity and gene expression changes in the earthworm Eisenia fetida (Savigny 1826). Despite being frequently exposed to multiple pesticides, including the common combination of abamectin (ABA) and carbendazim (CAR), environmental organisms have primarily been studied for the effects of individual pesticides. Acute toxicity results exhibited that the combination of ABA and CAR caused a synergistic impact on E. fetida. The levels of MDA, ROS, T-SOD, and caspase3 demonstrated a significant increase across most individual and combined groups, indicating the induction of oxidative stress and cell death. Additionally, the expression of three genes (hsp70, gst, and crt) exhibited a significant decrease following exposure to individual pesticides and their combinations, pointing toward cellular damage and impaired detoxification function. In contrast, a noteworthy increase in ann expression was observed after exposure to both individual pesticides and their mixtures, suggesting the stimulation of reproductive capacity in E. fetida. The present findings contributed to a more comprehensive understanding of the potential toxicity mechanisms of the ABA and CAR mixture, specifically on oxidative stress, cell death, detoxification dysfunction, and reproductive capacity in earthworms. Collectively, these data offered valuable toxicological insights into the combined effects of pesticides on soil organisms, enhancing our understanding of the underlying risks associated with the coexistence of different pesticides in natural soil environments.

Distribution, source apportionment, and ecological risk assessment of soil antibiotic resistance genes in urban green spaces

Urban green spaces play a crucial role in cities by providing near-natural environments that greatly impacts the health of residents. However, these green spaces have recently been scrutinized as potential reservoirs of antibiotic resistance genes (ARGs), posing significant ecological risks. Despite this concern, our understanding of the distribution, sources, and ecological risks associated with ARGs remains limited. In this study, we investigated the spatial distribution of soil ARGs using spatial interpolation and auto-correlation analysis. To apportion the source of soil ARGs in urban green spaces of Tianjin, Geo-detector method (GDM) was employed. Furthermore, we evaluated the ecological risk posed by ARGs employing risk quotients (RQ). The results of our study showed a significantly higher abundance of Quinolone resistance genes in the soil of urban green spaces in Tianjin. These genes were mainly found in the northwest, central, and eastern regions of the city. Our investigation identified three main factors contributing to the presence of soil ARGs: antibiotic production, precipitation, livestock breeding, and hospital. The results of ecological risk in RQ value showed a high risk associated with Quinolone resistance genes, followed by Aminoglycoside, Tetracycline, Multidrug, MLSB, Beta Lactam, Sulfonamide, and Chloramphenicol. Mantel-test and correlation analysis revealed that the ecological risk of ARGs was greatly influenced by soil properties and heavy metals. This study provides a new perspective on source apportionment and the ecological risk assessment of soil ARGs in urban green spaces.

Low-density polyethylene enhances the disturbance of microbiome and antibiotic resistance genes transfer in soil-earthworm system induced by pyraclostrobin

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.

Mechanisms Underlying the Overlooked Chiral Fungicide-Driven Enantioselective Proliferation of Antibiotic Resistance in Earthworm Intestinal Microbiome

From a "One Health" perspective, the global threat of antibiotic resistance genes (ARGs) is associated with modern agriculture practices including agrochemicals application. Chiral fungicides account for a considerable proportion of wildly used agrochemicals; however, whether and how their enantiomers lead to differential proliferation of antibiotic resistance in agricultural environments remain overlooked. Focused on the soil-earthworm ecosystem, we for the first time deciphered the mechanisms underlying the enantioselective proliferation of antibiotic resistance driven by the enantiomers of a typical chiral fungicide mandipropamid (i.e., R-MDP and S-MDP) utilizing a multiomic approach. Time-series metagenomic analysis revealed that R-MDP led to a significant enhancement of ARGs with potential mobility (particularly the plasmid-borne ARGs) in the earthworm intestinal microbiome. We further demonstrated that R-MDP induced a concentration-dependent facilitation of plasmid-mediated ARG transfer among microbes. In addition, transcriptomic analysis with verification identified the key aspects involved, where R-MDP enhanced cell membrane permeability, transfer ability, biofilm formation and quorum sensing, rebalanced energy production, and decreased cell mobility versus S-MDP. Overall, the findings provide novel insights into the enantioselective disruption of microbiome and resistome in earthworm gut by chiral fungicides and offer significant contributions to the comprehensive risk assessment of chiral agrochemicals in agroecosystems.

Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere

The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.

Effects of artificial sweetener acesulfame on soil-dwelling earthworms (Eisenia fetida) and its gut microbiota

Artificial sweeteners (AS) are the emerging contaminants with potential toxicity to living organisms. The effects of AS to soil typical invertebrates have not been revealed. In this study, the responses of earthworms (Eisenia fetida) and gut microbial communities to acesulfame-contaminated soils (0.1, 1 and 10 mg kg-1) were studied using transcriptomics, metabolomics and metagenomics analyses. The fresh weight of earthworms was significantly stimulated by acesulfame at concentrations of 1 mg kg-1. Sphingolipid metabolism, purine metabolism, cutin, suberine and wax biosynthesis pathways were significantly affected. At 10 mg kg-1 treatment, the amount and weight of cocoons were significantly increased and decreased, respectively, accompanied by the significant disorder of ECM-receptor interaction, and carbon fixation in photosynthetic organisms pathways. Lysosome pathway was significantly affected in all the treatments. Moreover, the acesulfame significantly increased the relative abundance of Bacteroidetes and Mucoromycota, and decreased Proteobacteria in the gut of earthworms. Our multi-level investigation indicated that AS at a relatively low concentration induced toxicity to earthworms and AS pollution has significant environmental risks for soil fauna.

Effects of Zinc Thiazole and Oxytetracycline on the Microbial Metabolism, Antibiotic Resistance, and Virulence Factor Genes of Soil, Earthworm Gut, and Phyllosphere

Pesticides and antibiotics are believed to increase the incidence of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), constituting a serious threat to global health. However, the impact of this combined pollution on the microbiome and that of the related ARGs and VFGs on soil-plant-animal systems remain unknown. In this study, a 60-day microcosm experiment was conducted to reveal the effects of zinc thiazole (ZT) and oxytetracycline (OTC) on microbial communities, antibiotic resistomes, and virulence factors in soil, earthworm gut, and phyllosphere samples using metagenomics. ZT exposure perturbed microbial communities and nutrient metabolism and increased the abundance of ARGs and VFGs in the gut. Combined exposure changed the profiles of ARGs and VFGs by decreasing microbial diversity in the phyllosphere. Host-tracking analysis identified some genera, such as Citrobacter and Aeromonas, as frequent hosts of ARGs and VFGs in the gut. Notably, some co-occurrence patterns of ARGs and MGEs were observed on the metagenome-assembled contigs. More importantly, ZT markedly increased the abundance of potentially drug-resistant pathogens Acinetobacter soli and Acinetobacter junii in the phyllosphere. Overall, this study expands our current understanding of the spread of ARGs and VFGs in soil-plant-animal systems under pollutant-induced stress and the associated health risks.

Long-term application of organic fertilizer prompting the dispersal of antibiotic resistance genes and their health risks in the soil plastisphere

Microplastic (MP) pollution is a rapidly growing global environmental concern that has led to the emergence of a new environmental compartment, the plastisphere, which is a hotspot for the accumulation of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, studies on the effects of long-term organic fertilizer application on the dispersal of ARGs and virulence factor genes (VFGs) in the plastisphere of farmland soil have been limited. Here, we performed a field culture experiment by burying nylon bags filled with MPs in paddy soil that had been treated with different fertilizers for over 30 years to explore the changes of ARGs and VFGs in soil plastisphere. Our results show that the soil plastisphere amplified the ARG and VFG pollution caused by organic fertilization by 1.5 and 1.4 times, respectively. And it also led to a 2.7-fold increase in the risk of horizontal gene transfer. Meanwhile, the plastisphere tended to promote deterministic process in the community assembly of HBPs, with an increase of 1.4 times. Network analysis found a significant correlation between ARGs, VFGs, and bacteria in plastisphere. Correlation analysis highlight the important role of mobile genetic elements (MGEs) and bacterial communities in shaping the abundance of ARGs and VFGs, respectively. Our findings provide new insights into the health risk associated with the soil plastisphere due ARGs and VFGs derived from organic fertilizers.

Chlorothalonil drives the antibiotic resistome in earthworm guts

Earthworms are recognized as carriers of pollutants; however, how fungicide residues affect microbiota and antibiotic resistance genes (ARGs) in earthworm guts has remained unclear. In this work, changes in the earthworm gut microbiome and resistome were investigated after chlorothalonil (CTL) application. Earthworm activity accelerated the dissipation of CTL in soil, while metagenomic analysis revealed that CTL altered the ARG profile, leading to an increased abundance of ARGs in earthworm guts, particularly with respect to ARG subtypes CRP and OXA-427. CTL also reduced bacterial diversity and elevated the relative abundance of the phylum Proteobacteria, including a potential ARG host, Aeromonas, which is a known pathogen. Various bacterial genera from the Actinobacteria and Proteobacteria phyla were identified as broad-spectrum hosts for ARGs in earthworm guts. CTL could increase the abundance of multidrug efflux pump genes and enhance the abundance of mobile genetic elements, especially plasmids. Various co-occurrence patterns between plasmids and ARGs were also found after CTL treatments. It is concluded that CTL may act as a selective stress for ARGs and lead to an increase in their abundance by facilitating the proliferation of potential ARG hosts and enhancing plasmid-mediated horizontal transfer frequency of ARGs in earthworm guts.

Stenotrophomonas pavanii DJL-M3 inoculated biochar stabilizes the rhizosphere soil homeostasis of carbendazim-stressed rice

Plant-microbe interactions have been effectively used in phytoremediation to reduce agrochemical contamination of crops and soils, but little information is available regarding the general effect of such association on rhizosphere soil homeostasis. In this study, we immobilized Stenotrophomonas pavanii DJL-M3, a carbendazim (CBZ)-degrading endophyte, in rice husk-derived biochar to control fungicide residue in the rice microenvironment. The influence of biochar inoculated with strain DJL-M3 on rhizobacterial communities was also investigated, including activity and fundamental function predictions. An adsorption kinetics test showed that strain DJL-M3 slowed the adsorption rate slightly without sacrificing the adsorption capacity of rice-husk biochar on CBZ. Immobilization in biochar helped S. pavanii DJL-M3 to establish an ecological niche in rhizosphere soils. This process significantly reduced CBZ levels in rice and rhizosphere soil while maintaining stable heterotrophic microbial respiration and carbon (C) metabolic activity. Soil amendment with the strain DJL-M3-biochar composite resulted in relatively little disturbance of fundamental soil functions, such as nitrogen (N) and sulfur (S) cycling, which explained the better plant growth and higher soil fertility observed with CBZ contamination. Overall, the combination of biochar and S. pavanii DJL-M3 demonstrated the potential to safeguard the microbiological environment of rice.

The ecological and molecular mechanism underlying effective reduction of antibiotic resistance genes pollution in soil by fermentation broth from fruit and vegetable waste

The strategies to relieve antibiotic resistance genes (ARGs) pollution are urgently needed. Fermentation broth from fruit and vegetable waste (FFVW), an agricultural amendment, exhibits a remarkable capacity to reduce ARG pollution; however, the underlying mechanism of this effect remains unclear. We performed microcosm experiments to reappear the phenomenon of FFVW-driven reduction in ARGs. Moderate-level FFVW reduced gene resistance to sulfonamide (41.2 %), macrolide-lincosamide-streptogramin (MLS) (47.2 %), chloramphenicol (63.2 %), and tetracycline (61.4 %). Binning and network analyses revealed that Actinobacteria comprise the primary hosts of ARGs in arable soil, and FFVW substantially inhibited the growth and metabolic activity of these organisms. Moreover, tetracycline and MLS production was partially/completely inhibited by FFVW, further reducing the transfer frequency by 52.9-86.1 % and 46.6-66.6 % in the intragenic and intergenic mating systems, respectively. Furthermore, the expression of genes related to conjugation pairing and plasmid transfer was downregulated. Thus, FFVW effectively reduces ARG pollution by inhibiting Actinobacteria proliferation, thereby reducing selective pressure and restricting horizontal gene transfer. Our findings highlight the important underlying mechanisms of FFVW involved in ARG reduction, supporting its use in arable soil.

Polyethylene mulch film-derived microplastics enhance the bioaccumulation of atrazine in two earthworm species (Eisenia fetida and Metaphire guillelmi) via carrier effects

Microplastics (MPs) may significantly affect the bioavailability of coexisting pollutants in soil by adsorption-desorption behavior. However, the mechanisms underlying these interaction remain unclear. Herein, the influence of unused polythylene mulch film-derived MPs (MFMPs) and farmland residual polyethylene mulch film-derived MPs (MFMPs-aged) on the adsorption-desorption behavior and bioavailability of atrazine (ATZ) in soil were investigated. The adsorption kinetics and the adsorption isotherms of ATZ on soil, MFMPs, and MFMPs-aged fitted well by the pseudo-second-order model and the Langmuir model, respectively. ATZ were easier to desorb from soil, MFMPs, and MFMPs-aged in the simulated earthworm digestive fluid than that in the CaCl₂ solution. The adsorption and desorption capacities of MFMPs and MFMPs-aged for ATZ were higher than those of soil, especially for MFMPs-aged. The existence of MPs in soil strengthened the adsorption and desorption capacities of ATZ, and the strengthened effects were promoted by the addition amount and aging process of MPs. Moreover, the occurrence of MPs significantly increased the bioaccumulation of ATZ in earthworms, especially for MFMPs-aged. This study deepens the knowledge of the interaction mechanisms of mulch film-derived MPs and pesticide pollution.

Exposure to cypermethrin pesticide disturbs the microbiome and disseminates antibiotic resistance genes in soil and the gut of Enchytraeus crypticus

Worldwide, pyrethroids, such as cypermethrin, are the second most applied group of insecticides, however, their effects on the soil microbiome and non-target soil fauna remain largely unknown. Herein, we assessed the change of bacterial communities and antibiotic resistance genes (ARGs) of soil and in the gut of the model soil species Enchytraeus crypticus using a combination of 16S rRNA gene amplicon sequencing, and high-throughput qPCR of ARGs. Results indicate that cypermethrin exposure enriches potential pathogens (e.g. Bacillus anthracis) in the soil and gut microbiome of E. crypticus, heavily disrupting the latter's microbiome structure, and even disrupts activities of the E. crypticus immune system. The co-occurrence of potential pathogens (e.g. Acinetobacter baumannii), ARGs, and mobile genetic elements (MGEs) revealed the increased risk of pathogenicity as well as antibiotic resistance in potential pathogens. Moreover, structural equation modeling demonstrated that the dissemination of ARGs was not only promoted by MGEs, but also by the ratio of the core to non-core bacterial abundance. Collectively, these results provide an in-depth view of the previously unappreciated environmental risk of cypermethrin on the dissemination of ARGs in the soil and non-target soil fauna.

A novel bidirectional regulation mechanism of mancozeb on the dissemination of antibiotic resistance

The high abundance of antibiotic resistance genes (ARGs) in the fungicide residual environment, posing a threat to the environment and human health, raises the question of whether and how fungicide promotes the prevalence and dissemination of antibiotic resistance. Here, we reported a novel mechanism underlying bidirectional regulation of a typical heavy-metal-containing fungicide mancozeb on the horizontal transfer of ARGs. Our findings revealed that mancozeb exposure significantly exerted oxidative and osmotic stress on the microbes and facilitated plasmid-mediated ARGs transfer, but its metallic portions (Mn and Zn) were potentially utilized as essential ions by microbes for metalating enzymes to deal with cellular stress and thus reduce the transfer. The results of transcriptome analysis with RT-qPCR confirmed that the expression levels of cellular stress responses and conjugation related genes were drastically altered. It can be concluded mancozeb bidirectionally regulated the ARGs dissemination which may be attributed to the diverse effects on the microbes by its different portions. This novel mechanism provides an updated understanding of neglected fungicide-triggered ARGs dissemination and crucial insight for comprehensive risk assessment of fungicides.

Toxicity sharing model of earthworm intestinal microbiome reveals shared functional genes are more powerful than species in resisting pesticide stress

Earthworm intestinal bacteria and indigenous soil bacteria work closely during various biochemical processes and play a crucial role in maintaining the internal stability of the soil environment. However, the response mechanism of these bacterial communities to external pesticide disturbance is unknown. In this study, soil and earthworm gut contents were metagenomically sequenced after exposure to various concentrations of nitrochlorobenzene (0-1026.7 mg kg^-1). A high degree of similarity was found between the microbial community composition and abundance in the worm gut and soil, both of which decreased significantly (P < 0.05) under elevated pesticide stress. The toxicity sharing model (TSM) showed that the toxicity sharing capacity was 97.4-125.7 % and 100.4-130.2 % for E_genes (genes in the worm gut) and E_met(degradation genes in the worm gut) in the earthworm intestinal microbiome, respectively. This indicated that the earthworm intestinal microbiome assisted in relieving the pesticide toxicity of the indigenous soil microbiome. This study showed that the TSM could quantitatively describe the toxic effect of pesticides on the earthworm intestinal microbiome. It provides a new analytical model for investigating the ecological alliance between earthworm intestinal microbiome and indigenous soil microbiome under pesticide stress while contributing a more profound understanding of the potential to use earthworms to mitigate pesticide pollution in soils and develop earthworm-based soil remediation techniques.

Performance and mechanisms of biochar-assisted vermicomposting in accelerating di-(2-ethylhexyl) phthalate biodegradation in farmland soil

Biochar and earthworms can accelerate di-(2-ethylhexyl) phthalate (DEHP) degradation in soils. However, little is known regarding the effect of biochar-assisted vermicomposting on soil DEHP degradation and the underlying mechanisms. Therefore, the present study investigated DEHP degradation performance and bacterial community changes in farmland soils using earthworms, biochar, or their combination. Biochar-assisted vermicomposting significantly improved DEHP degradation through initial physical adsorption on biochar and subsequent rapid biodegradation in the soil, earthworm gut, and charosphere. Burkholderiaceae, Pseudomonadaceae, and Flavobacteriaceae were the potential DEHP degraders and were enriched in biochar-assisted vermicomposting. In particularly, Burkholderiaceae and Sphingomonadaceae were enriched in the earthworm gut and charosphere, possibly explaining the mechanism of accelerated DEHP degradation in biochar-assisted vermicomposting. Soil pH, soil organic matter, and humus (humic acid, fulvic acid, and humin) increased by earthworms or biochar enhanced DEHP degradation. These findings imply that biochar-assisted vermicomposting enhances DEHP removal not only through rapid physical sorption but also through the improvement of soil physicochemical characteristics and promotion of degraders in the soil, earthworm gut, and charosphere. Overall, biochar-assisted vermicomposting is a suitable method for the remediation of organic-contaminated farmland soils.

Tracking antibiotic resistance genes in microplastic-contaminated soil

Agricultural soils and microplastics (MPs) are hotspots for antibiotic resistance genes (ARGs). Plastic mulch is the most important source of MPs in agricultural soil. ARGs, mobile genetic elements (MGEs), and their host profiles in long-term mulch MP-exposed soils remain unclear. In the present study, metagenomics was used to investigate the distribution patterns of ARGs and MGEs in eight Chinese provinces with a long history of plastic mulch use. A total of 204 subtypes of ARGs and thousands of MGEs (14 integrons, 28 insertions, and 2993 plasmids) were identified. A similar diversity of ARGs was found among MPs film-contaminated sites. The types of ARGs with a high abundance were more concentrated, and multidrug resistance genes were the dominant ARGs. Soils from regions with a longer history of plastic film use (such as Xinjiang province) had a higher abundance of ARGs and MGEs. The distribution of ARGs and MGEs exhibited a modular network distribution pattern. A total of 27 ARG subtypes and 29 MGEs showed co-occurrence network relationships. More than 10 common hosts of ARGs and MGEs, such as Pseudomonas, were found, and their abundances were highest in three provinces, including Xinjiang. This study may help elucidate the impact mechanism of long-term MP residues on the occurrence and spread of ARGs in soil.