Combined pollution of arsenic and Polymyxin B enhanced arsenic toxicity and enriched ARG abundance in soil and earthworm gut microbiotas

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.

Geographic and environmental impacts on gut microbiome in Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita)

Introduction

Gut microbiome plays a crucial role in the health of wild animals. Their structural and functional properties not only reflect the host's dietary habits and habitat conditions but also provide essential support for ecological adaptation in various environments.

Methods

This study investigated the gut microbiome of Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita) across different geographic regions using 16S rRNA gene and metagenomic sequencing.

Results

Results showed distinct clustering patterns in gut microbiota based on geographic location. Soil had an insignificant impact on host gut microbiome. Himalayan langurs from mid-altitude regions exhibited higher levels of antibiotic resistance genes associated with multidrug resistance, while Xizang macaques from high-altitude regions showed a broader range of resistance genes. Variations in carbohydrate-active enzymes and KEGG pathways indicated unique metabolic adaptations to different environments.

Discussion

These findings provide valuable insights into the health and conservation of these primates and the broader implications of microbial ecology and functional adaptations in extreme conditions.

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.

Microbial-influenced pesticide removal co-occurs with antibiotic resistance gene variation in soil-earthworm-maize system

Within human-influenced landscapes, pesticides cooccur with a variety of antibiotic stressors. However, the relationship between pesticides removal process and antibiotic resistance gene variation are not well understood. This study explored pesticide (topramezone, TPZ) and antibiotic (polymyxin E, PME) co-contamination using liquid chromatography-tandem mass spectrometry (LC-MS/MS), bacterial-16 S rRNA sequencing and high-throughput quantitative polymerase chain reaction (HT-qPCR) in a soil-earthworm-maize system. After incubating soil for 28 days with TPZ and PME (10 mg kg-1 dry weight), earthworm weight-gain, mortality rates, and maize plant weight-gain only differed slightly, but height-gain significantly decreased. PME significantly increased TPZ-removal in the soil. Accumulation of TPZ in earthworm's tissues may pose potential risks in the food chain. Combined pollution altered the microbial community structure and increased the abundance of functional microorganisms involved in aromatic compound degradation. Furthermore, maize rhizosphere can raise resistance genes, however earthworms can reduce resistance genes. Co-contamination increased absolute abundance of mobile genetic elements (MGEs) in bulk-soil samples, antibiotic resistance genes (ARGs) in skin samples and number of ARGs in bulk-soil samples, while decreased absolute abundance of transposase gene in bulk-soil samples and number of ARGs in rhizosphere-soil samples. Potential hosts harbouring ARGs may be associated with the antagonistic effect during resistance and detoxification of TPZ and PMB co-occurrence. These findings provide insights into the mechanism underlining pesticide removal regarding occurrence of ARGs in maize agroecosystem.

Prioritized regional management for antibiotics and heavy metals in animal manure across China

High levels of antibiotics and heavy metals in animal manure pose a potential threat to both the ecological environment and public health. A regional knowledge of their distribution and risk assessment across China remains unclear. A dataset containing 4082 records covering a total of forty-two antibiotics and eight heavy metals was established for animal manure across China. The results showed that the residual concentration of antibiotics was in the order of tetracyclines > aminoglycosides > fluoroquinolones > macrolides > sulfonamides > β-lactams, and that of heavy metals is Zn > Cu > Cr > Pb > Ni > As > Cd > Hg. The mean concentration of antibiotics and heavy metals was higher in pig manure compared to chicken and cow manure (Kruskal-Wallis test). The lowest level of antibiotics was observed in Northwest China based on geographic distribution characteristics. It was related to the high ratio of cow and sheep farming that less antibiotics were administered to. The pollution status of heavy metals was more severe in East China. Furthermore, high correlations were observed between antibiotics (tetracyclines) and heavy metals (Cu, Zn, and As). Especially, tetracycline in North China and Cd in Northeast China exhibited a high risk in manure; thus, they were priority regions for antibiotics/heavy metals pollution control. This study identified risk assessment of typical antibiotics and heavy metals in animal manure and emphasized the necessity of regional management across China.

Elimination of antibiotic-resistant bacteria and resistance genes by earthworms during vermifiltration treatment of excess sludge

Vermifiltration (VF) and a conventional biofilter (BF, no earthworm) were investigated by metagenomics to evaluate the removal rates of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and class 1 integron-integrase (intI1), as well as the impact mechanism in combination with the microbial community. According to the findings of qPCR and metagenomics, the VF facilitated greater removal rates of ARGs (78.83% ± 17.37%) and ARB (48.23% ± 2.69%) than the BF (56.33% ± 14.93%, 20.21% ± 6.27%). Compared to the control, the higher biological activity of the VF induced an increase of over 60% in the inhibitory effect of earthworm coelomic fluid on ARB. The removal rates of ARGs by earthworm guts also reached over 22%. In addition, earthworms enhanced the decomposition of refractory organics, toxic, and harmful organics, which led to a lower selective pressure on ARGs and ARB. It provides a strategy for reducing resistant pollution in sewage treatment plants and recognizing the harmless stability of sludge.

Gut microbiota and transcriptome response of earthworms (Metaphire guillelmi) to polymyxin B exposure

Polymyxin B (PMB) has received widespread attention for its use as a last-line therapy against multidrug-resistant bacterial infection. However, the consequences of unintended PMB exposure on organisms in the surrounding environment remain inconclusive. Therefore, this study investigated the effects of soil PMB residue on the gut microbiota and transcriptome of earthworms (Metaphire guillelmi). The results indicated that the tested doses of PMB (0.01-100 mg/kg soil) did not significantly affect the richness and Shannon's diversity index of the earthworm gut microbiota, but PMB altered its community structure and taxonomic composition. Moreover, PMB significantly affected Lysobacter, Aeromonas, and Sphingomonas in the soil microbiota, whereas Pseudomonas was significantly impacted the earthworm gut microbiota. Furthermore, active bacteria responded more significantly to PMB than the total microbial community. Bacterial genera such as Acinetobacter and Bacillus were highly correlated with differential expression of some genes, including up-regulated genes associated with folate biosynthesis, sulphur metabolism, and the IL-17 signalling pathway, and downregulated genes involved in vitamin digestion and absorption, salivary secretion, other types of O-glycan biosynthesis, and the NOD-like receptor signalling pathway. These results suggest that adaptation to PMB stress by earthworms involves changes in energy metabolism, their immune and digestive systems, as well as glycan biosynthesis. The study findings help elucidate the relationship between earthworms and their microbiota, while providing a reference for understanding the environmental risks of PMB.

Dietary exposure to sulfamethazine alters fish intestinal homeostasis and promotes resistance gene transfer

The present study was undertaken to explore the effects of sulfamethazine (SMZ) dietary exposure on the enrichment of the intestine microbial structure, and antibiotic resistance gene (ARGs) transmission in marine medaka, with respect to antibiotic dose, duration, and sex. In male fish, a dietary exposure of 10 μg/L SMZ led to a heightened SMZ enrichment in the intestine, whereas metabolite (N-SMZ) levels were elevated at a higher exposure concentration (100 μg/L). Conversely, female fish exhibited stable levels of accumulation and metabolic rates across the exposure period. The composition of intestinal microorganisms revealed that exposure duration exerted a greater impact on the abundance and diversity of gut microbes, and microbial responses to SMZ varied across exposure time points. The expansion of Bacteroidetes and Ruegeria likely stimulated SMZ metabolism and contributed to the more balanced level of SMZ and N-SMZ observed in females. In males, short-term SMZ stress resulted in a disruption of intestinal homeostasis, while the rise in the abundance of the Fusobacteria and Propionigeniuma suggested a potential enhancement in intestinal anti-inflammatory capacity over time. Overall, female medaka exhibited greater adaptability to SMZ, and males appear to experience prolonged effects due to SMZ. A total of 11 ARGs and 5 mobile genetic elements (MGEs) were identified. Ruegeria is the main carrier of two types of MGEs (IS1247, ISSm2-Xanthob), and may serve as an indicator of ARG transmission. Therefore, it is rational to consider some fish breeding areas in natural waters as potential "reservoirs" of antibiotic resistance. This research will provide a valuable reference for the transmission of drug resistance along the food chain.

Enantioselective effect of the chiral fungicide tebuconazole on the microbiota community and antibiotic resistance genes in the soil and earthworm gut

Tebuconazole, consisting of two enantiomers, has a high detectable rate in the soil. The residue of tebuconazole in the soil may cause risk to microbiota community. Antibiotic resistance genes (ARGs) are considered as emerging environmental contaminants, and they can be transferred vertically and horizontally between microbiota community in the soil. Until now, the enantioselective effect of tebuconazole on the microbiota community and ARGs in the soil and earthworm gut has remained largely unknown. Tebuconazole enantiomers showed different bioconcentration behaviors in earthworms. The relative abundances of bacteria belonging to Actinobacteriota, Crenarchaeota and Chloroflexi in R-(-)-tebuconazole-treated soil were higher than those in S-(+)-tebuconazole-treated soil at same concentrations. In the earthworm gut, bacteria belonging to Proteobacteria and Bacteroidota exhibited different relative abundances between the S-(+)-tebuconazole and R-(-)-tebuconazole treatments. The numbers and abundances of ARGs in the soil treated with fungicides were higher than those in the control. In earthworm gut, the diversities of ARGs in all treatments were higher than that in the control, and the relative abundances of Aminoglycoside, Chloramphenicol, Multidrug resistance genes and mobile genetic elements (MGEs) in R-(-)-tebuconazole-treated earthworm gut were higher than those in S-(+)-tebuconazole-treated earthworm gut. Most of ARGs showed a significantly positive correlation with MGEs. Based on network analysis, many ARGs may be carried by bacteria belonging to Bacteroidota and Proteobacteria. These results provide valuable information for understanding the enantioselective effect of tebuconazole on the microbiota community and ARGs.

Toxic effects of long-term dual or single exposure to oxytetracycline and arsenic on Xenopus tropicalis living in duck wastewater

Direct discharge of aquaculture wastewater may have toxic effects, due to the presence of heavy metals, antibiotics, and even resistant pathogens, but little attention has been given. Here, tanks simulating a wild ecosystem were built to study the effects of long-term exposure to duck wastewater containing oxytetracycline (OTC) and/or arsenic (As) on the growth, physiological function, and gut microbiota evolution of Xenopus tropicalis. The results showed that duck wastewater had no apparent impact on X. tropicalis, but the impact increased significantly (P < 0.05) with exposure to OTC and/or As, especially the impact on body weight and growth rate. Biochemical indicators revealed varying degrees of oxidative stress damage, hepatotoxicity (inflammation, necrosis, and sinusoids), and collagen fibrosis of X. tropicalis in all treated groups after 72 days of exposure, which indirectly inhibited X. tropicalis growth. Moreover, 16S rDNA amplicon sequencing results showed that the gut microbiota structure and metabolic function were perturbed after chronic exposure, which might be the leading cause of growth inhibition. Interestingly, the abundance of intestinal resistance genes (RGs) increased with exposure time owing to the combined direct and indirect effects of stress factors in duck wastewater. Moreover, once the RGs were expressed, the resistance persisted for at least 24 days, especially that conferred by tetA. These results provide evidence of the toxic effects of DW containing OTC (0.1-4.0 mg/L) and/or As (0.3-3.5 µg/L) on amphibians and indicate that it is vital to limit the usage of heavy metals and antibiotics on farms to control the biotoxicity of wastewater.

How do different arsenic species affect the joint toxicity of perfluorooctanoic acid and arsenic to earthworm Eisenia fetida: A multi-biomarker approach

Perfluorooctanoic acid (PFOA) and arsenic are widely distributed pollutants and can coexist in the environment. However, no study has been reported about the effects of different arsenic species on the joint toxicity of arsenic and PFOA to soil invertebrates. In this study, four arsenic species were selected, including arsenite (As(III)), arsenate (As(V)), monomethylarsonate (MMA), and dimethylarsinate (DMA). Earthworms Eisenia fetida were exposed to soils spiked with sublethal concentrations of PFOA, different arsenic species, and their binary mixtures for 56 days. The bioaccumulation and biotransformation of pollutants, as well as eight biomarkers in organisms, were assayed. The results indicated that the coexistence of PFOA and different arsenic species in soils could enhance the bioavailability of arsenic species while reducing the bioavailability of PFOA, and inhibit the arsenic biotransformation process in earthworms. Responses of most biomarkers in joint treatments of PFOA and As(III)/As(V) showed more significant variations compared with those in single treatments, indicating higher toxicity to the earthworms. The Integrated Biomarker Response (IBR) index was used to integrate the multi-biomarker responses, and the results also exhibited enhanced toxic effects in combined treatments of inorganic arsenic and PFOA. In comparison, both the biomarker variations and IBR values were lower in joint treatments of PFOA and MMA/DMA. Then the toxic interactions in the binary mixture systems were characterized by using a combined method of IBR and Effect Addition Index. The results revealed that the toxic interactions of the PFOA/arsenic mixture in earthworms depended on the different species of arsenic. The combined exposure of PFOA with inorganic arsenic led to a synergistic interaction, while that with organic arsenic resulted in an antagonistic response. Overall, this study provides new insights into the assessment of the joint toxicity of perfluoroalkyl substances and arsenic in soil ecosystems.

Damage and elimination of soil and water antibiotic and heavy metal pollution caused by livestock husbandry

The combination of antibiotics and heavy metals (HMs) increases the toxicity range of influence and requires additional research attention. This article analyzed the toxicity mechanisms and damage of combined pollution. Cross-resistance, co-resistance, and co-regulation are the primary toxicity mechanisms. Combined pollution increases antibiotic resistance genes (ARGs), increases bacterial resistance, and promotes the horizontal transfer of ARGs, affecting the types and distribution of microorganisms. The hazard of combined pollution varies with concentration and composition. The physicochemical and biological technologies for eliminating combined pollution are primarily elaborated. Adsorption, photocatalytic degradation, and microbial treatment show high removal rates and good recyclability, indicating good application potential. This review provides a basis and reference for the further study the elimination of combined antibiotic and HM pollution.

Response of Antibiotic Resistance Genes and Related Microorganisms to Arsenic during Vermicomposting of Cow Dung

Antibiotic resistance pollution in livestock manure is a persistent issue that has drawn public attention. Vermicomposting is an ecofriendly biological process that can render livestock manure harmless and resourceful. However, little is known about the impact of vermicomposting on antibiotic resistance in livestock manure under stress caused by potentially toxic arsenic levels. Herein, lab-scale vermicomposting was performed to comprehensively evaluate the shift in antibiotic resistance genes (ARGs) and related microorganisms in fresh earthworm casts as well as vermicompost product health (i.e., nutrient availability and enzyme activity) when they were fed on arsenic-contaminated cow manure. The results showed that the earthworms' interaction with cow dung led to a significant reduction in ARG concentrations, especially for tetracycline ARGs (tet-ARGs), β-lactam ARGs (bla-ARGs), and quinolone ARGs (qnr-ARGs). However, arsenic significantly enhanced ARG accumulation in earthworm casts in a dose-dependent manner. Moreover, vermicomposting increased the percentage of Bacteroidota in the converted products. Furthermore, arsenic exposure at low concentrations promoted the proliferation of Proteobacteria, whereas high concentrations had little effect on Proteobacteria. Our study provides valuable insight into the changes in the antibiotic resistome and related microorganisms during vermicomposting of arsenic-amended cow manure, and it is crucial to explain the environmental impact of earthworms and improve our understanding of the reciprocal benefits of soil invertebrates.

Carbendazim shapes microbiome and enhances resistome in the earthworm gut

BACKGROUND

It is worrisome that several pollutants can enhance the abundance of antibiotic resistance genes (ARGs) in the environment, including agricultural fungicides. As an important bioindicator for environmental risk assessment, earthworm is still a neglected focus that the effects of the fungicide carbendazim (CBD) residues on the gut microbiome and resistome are largely unknown. In this study, Eisenia fetida was selected to investigate the effects of CBD in the soil-earthworm systems using shotgun metagenomics and qPCR methods.

RESULTS

CBD could significantly perturb bacterial community and enrich specific bacteria mainly belonging to the phylum Actinobacteria. More importantly, CBD could serve as a co-selective agent to elevate the abundance and diversity of ARGs, particularly for some specific types (e.g., multidrug, glycopeptide, tetracycline, and rifamycin resistance genes) in the earthworm gut. Additionally, host tracking analysis suggested that ARGs were mainly carried in some genera of the phyla Actinobacteria and Proteobacteria. Meanwhile, the level of ARGs was positively relevant to the abundance of mobile genetic elements (MGEs) and some representative co-occurrence patterns of ARGs and MGEs (e.g., cmx-transposase and sul1-integrase) were further found on the metagenome-assembled contigs in the CBD treatments.

CONCLUSIONS

It can be concluded that the enhancement effect of CBD on the resistome in the earthworm gut may be attributed to its stress on the gut microbiome and facilitation on the ARGs dissemination mediated by MGEs, which may provide a novel insight into the neglected ecotoxicological risk of the widely used agrochemicals on the gut resistome of earthworm dwelling in soil. Video abstract.

Diverse antibiotic resistance genes and potential pathogens inhabit in the phyllosphere of fresh vegetables

Fresh vegetables are considered as a reservoir of pathogenic bacteria and antibiotic resistance genes (ARGs), which are the emerging environmental contaminants, posing increasing concerned risk to human health. However, the prevalence of pathogens in phyllosphere of fresh vegetables, as well as the association of ARGs with pathogenic bacteria, have not been well elaborated. In this study, we explored the structure of microbial communities and ARGs through high-throughput quantitative PCR and 16S rRNA gene Illumina sequencing, and characterized the microorganisms resisting to antibiotics by pure culture. From phyllosphere of six different kinds of vegetables, 205 ARGs were detected and genes for multidrug resistance was the most abundant. The predominant potential pathogens were classified to Pseudomonas, Klebsiella, and Acinetobacter genera, which carried various ARGs such as multidrug and beta-lactam resistance genes presumedly. Among six kinds of vegetables, Lactuca sativa var. asparagina carried the highest abundance of potential pathogens and ARGs, while Allium sativum L harbored the lowest abundance of pathogens and ARGs. In addition, various culturable bacteria resisting to colistin or meropenem could be isolated from all vegetables, remarkably, all the isolates resistant to both antibiotics are potential pathogens. Our study highlighted the risks of pathogens and ARGs from raw vegetables to consumers, characterized their structure patterns among different vegetables, and analyzed the potential mechanisms regulating phyllosphere pathogens and resistome of fresh vegetables, which would be helpful for reducing the microbial risk from vegetable ingestion.

Earthworms as candidates for remediation of potentially toxic elements contaminated soils and mitigating the environmental and human health risks: A review

Global concerns towards potentially toxic elements (PTEs) are steadily increasing due to the significant threats that PTEs pose to human health and environmental quality. This calls for immediate, effective and efficient remediation solutions. Earthworms, the 'ecosystem engineers', can modify and improve soil health and enhance plant productivity. Recently, considerable attention has been paid to the potential of earthworms, alone or combined with other soil organisms and/or soil amendments, to remediate PTEs contaminated soils. However, the use of earthworms in the remediation of PTEs contaminated soil (i.e., vermiremediation) has not been thoroughly reviewed to date. Therefore, this review discusses and provides comprehensive insights into the suitability of earthworms as potential candidates for bioremediation of PTEs contaminated soils and mitigating environmental and human health risks. Specifically, we reviewed and discussed: i) the occurrence and abundance of earthworms in PTEs contaminated soils; ii) the influence of PTEs on earthworm communities in contaminated soils; iii) factors affecting earthworm PTEs accumulation and elimination, and iv) the dynamics and fate of PTEs in earthworm amended soils. The technical feasibility, knowledge gaps, and practical challenges have been worked out and critically discussed. Therefore, this review could provide a reference and guidance for bio-restoration of PTEs contaminated soils and shall also help developing innovative and applicable solutions for controlling PTEs bioavailability for the remediation of contaminated soils and the mitigation of the environment and human risks.