Network complexity of bacterial community driving antibiotic resistome in the microbiome of earthworm guts under different land use patterns

The combination of microplastics and glyphosate affects the microbiome of soil inhabitant Enchytraeus crypticus

Microplastics and pesticides are emerging contaminants that threaten soil ecosystems, yet their combined effects on soil health and soil fauna remain poorly understood. In this study, we constructed a microcosm to assess the individual and combined effects of microplastics and glyphosate on soil physicochemical properties, microbial communities, and the gut microbiome of soil invertebrates (Enchytraeus crypticus). Biodegradable polylactic acid (PLA) and conventional polyethylene terephthalate (PET) were introduced at environmentally relevant concentrations. Our results revealed that PLA had a stronger disruptive effect on soil microbial communities than PET, altering microbial diversity and functional composition. Glyphosate, in contrast, primarily influenced the gut microbiome of E. crypticus, reducing microbial diversity and inducing oxidative stress. Combined exposure to microplastics and glyphosate significantly intensified oxidative stress but did not amplify microbial dysbiosis beyond the effects of microplastics alone. Compare to PET, PLA combined with glyphosate had the most pronounced effects on both soil and gut microbiomes, suggesting that biodegradable microplastics may pose greater ecological risks than conventional microplastics when used alongside pesticides. These findings underscore the need for a reassessment of biodegradable plastic use in agriculture and highlight the complex interactions between microplastics and pesticides in shaping soil ecosystem health.

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.

Polystyrene microplastic exposure induces selective accumulation of antibiotic resistance genes in gut microbiota and its potential health risks

As emerging pollutants, antibiotic resistance genes (ARGs) and microplastics threaten the environment and human health. Gut microbiota is a hotspot for ARG emergence and spread. However, effects of microplastic exposure on the emergence and spread of gut microbial ARGs are unclear. Therefore, metagenomics was used to characterize polystyrene microplastics (PS)-induced ARG alterations in rat gut microbiota and their health risks, and to identify key ARG hosts and pathways as intervention targets. We found that PS exposure not only induced selective accumulation of glycopeptide and aminoglycoside ARGs, but also promoted mobility risks of glycopeptide and macrolide-lincosamide-streptogramin ARGs in gut microbiota. Metagenomic reassembly identified microbes belonging to Firmicutes (particularly order Clostridiales, such as speices Lachnospiraceae bacterium 3-1 and MD335) as major ARG hosts. Meanwhile, genera Enterococcus, Clostridioides and Streptococcus were main ARG hosts among human pathogens. Furthermore, glycopeptide and aminoglycoside ARGs were highly correlated with VanS/VanR signaling and its regulatory pathways of vancomycin resistance and peptidoglycan metabolism, amino sugar and nucleotide sugar metabolism, and CpxR signaling and its regulatory remodeling of cell envelope peptidoglycans and proteins in gut microbiota upon PS exposure. This study provides novel insights and intervention targets involved in PS-induced changes in gut microbial ARGs and their health risks.

The Mechanisms of Tetracycline in Shaping Antibiotic Resistance Gene Dynamics in Earthworm Casts During Vermicomposting

Earthworm gut digestion plays a crucial role in reducing antibiotic resistance genes (ARGs) during vermicomposting, offering significant potential for controlling ARG dissemination in livestock manure. However, the impact of residual tetracycline antibiotics on this process remains poorly understood. Herein, this study systematically evaluated the impact of tetracycline of three concentrations (0, 10, and 100 mg/kg) on ARG dynamics and microbial community evolution during 35-day vermicomposting of cattle manure. The results demonstrated that earthworm intestinal digestion effectively eliminated over 96% of initial ARG load in raw manure. Noticeably, tetracycline stress significantly enhanced total ARG abundance in the casts (p < 0.05), with distinct response patterns observed among different ARG types. Mechanistic analysis revealed that tetracycline potentially enhanced ARG persistence through two pathways: (1) promoting horizontal transfer via mobile genetic elements, and (2) altering gut microbial succession patterns that influence ARG host-microbe relationships. These discoveries contribute to our comprehension of antibiotic interference in vermi-remediation processes and provide insights for optimizing ARG mitigation strategies in contaminated livestock manure.

Vermicomposting significantly reduced antibiotic resistance genes in cow manure even under high tetracycline concentrations

Minimizing antibiotic resistance genes (ARGs) in livestock manure is crucial for curbing ARG dissemination. Vermicomposting can eliminate ARGs, but the effect of residual antibiotics on its reduction efficacy remains unclear. Herein, Eisenia foetida was employed to convert cow manure with varying concentrations of tetracycline (i.e., 0, 10, 100 mg/kg), aiming to explore the impact of tetracycline on ARG fate during vermicomposting for 35 days. Results showed that the total ARG abundance in vermicomposting (0.05 copies/16S rRNA copies) was significantly lower than that in natural composting (0.06 copies/16S rRNA copies) (p < 0.05). Notably, exposure to tetracycline increased total ARG abundance (p < 0.05) and stimulated microbial succession during vermicomposting, with some ARGs increasing and others decreasing. But ARGs removal in vermicomposting was still higher even under tetracycline stress than that in natural composting. Overall, vermicomposting is an effective method for reducing ARGs in cow manure even at high tetracycline levels.

Distinctive gut antibiotic resistome, potential health risks and underlying pathways upon cerebral ischemia-reperfusion injury

Antibiotic resistance genes (ARGs) as emerging pollutants pose health risks to humans and the environment. Gut microbiota is an important reservoir for ARGs and hotspot for ARG acquisition and dissemination. Non-antibiotic factors (such as disease pathophysiology) affect ARG emergence and dissemination. Cerebral ischemia-reperfusion injury (I/R) commonly occurs in stroke patients. However, effects of I/R on ARG emergence and dissemination are unknown. Therefore, metagenomics was used to unveil selective collection of gut antibiotic resistome and its health risks, key ARG hosts and underlying pathways upon I/R. Changes in gut antibiotic resistome upon I/R were characterized by tetracycline ARG accumulation and decreases in aminoglycoside and glycopeptide ARGs. Besides, changes in gut antibiotic resistome were corrected with those in gut microbiota from phylum to species, serum lipid accumulation and glucose depletion upon I/R. Additionally, health risks of gut microbial multidrug ARGs (such as abem, adek and TolC), macA, aph(3')-I and carO, co-localized with mobile gene elements, were increased upon I/R. Moreover, phyla Firmicutes (especially order Eubacteriales, class Clostridia) and Bacteroidota were key ARG hosts in gut microbiota of I/R gerbils. Furthermore, suppression of vancomycin resistance, and lantibiotic biosynthesis and immunity, disturbances in peptidoglycan biosynthesis and hydrolysis, activation of antimicrobial peptide resistance, lipopolysaccharide biosynthesis, teichoic acid biosynthesis, arabinogalactan biosynthesis, aromatic compound degradation, oxidative phosphorylation, the tricarboxylic acid cycle and its anaplerotic pathways were observed in upon I/R. This study provides novel insights and intervention targets related to selective collection of gut antibiotic resistome and its potential health risks upon I/R.

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.

Litter quality modulates changes in bacterial and fungal communities during the gut transit of earthworm species of different ecological groups

Earthworms are keystone animals stimulating litter decomposition and nutrient cycling. However, earthworms comprise diverse species which live in different soil layers and consume different types of food. Microorganisms in the gut of earthworms are likely to contribute significantly to their ability to digest organic matter, but this may vary among earthworm species. Here, we analyse the effect of food (litter) quality on gut microbiota and their changes during the gut passage (from foregut to hindgut) of earthworms of different ecological groups. The endogeic (soil living) species Aporrectodea caliginosa and the anecic (litter feeding) species Lumbricus terrestris were fed with high- (rape leaves) and low-quality litter (wheat straw) in a microcosm experiment for 18 weeks. Irrespective of earthworm species, alpha diversity of bacterial and fungal communities changed little during the gut passage, with the composition and diversity of microbial communities in the gut generally resembling those in soil more than in litter. In addition, the low-quality litter supported higher alpha diversity and more complex communities than high-quality litter. Further, gut microbial communities of the anecic L. terrestris changed less during gut passage than those of the endogeic A. caliginosa, especially when fed low-quality litter. Our findings indicate that earthworm gut microbial communities are predominantly shaped by the soil they ingest, but are modulated by the quality of litter they feed on and earthworm ecological group. Overall, the results suggest that earthworms primarily influence soil microbiota by mixing and spreading microorganisms from different microhabitats through bioturbation rather than by digesting microorganisms.

Biochar Reduced the Risks of Human Bacterial Pathogens in Soil via Disturbing Quorum Sensing Mediated by Persistent Free Radicals

Biochar has great potential in reducing the abundance of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) from soil. However, its efficiency in removing other biological pollutants, such as human bacterial pathogens (HBPs) and virulence factor genes (VFGs), is rarely studied. Herein, by pyrolyzing rice straw (RS) and pine wood (PW) at 350 and 700 °C, we prepared a series of biochar (RS350, RS700, PW350, and PW700) and investigated their impacts on the abundance and pathogenicity of HBPs. Compared with PW biochar, RS biochar effectively reduced the abundance of HBPs by 6.3-40.1%, as well as their pathogenicity, evidenced by an 8.2-10.1% reduction in the abundance of VFGs. Mechanistically, more persistent free radicals (PFRs) were formed in RS biochar than that of PW biochar during pyrolysis, and PFRs triggered the degradation of N-butyryl-l-homoserine lactone (C4-HSL) from 1.05 to 0.68 ng/kg, thereby disturbing the quorum sensing (QS) of HBPs. Once the QS was disturbed, the communications among HBPs were hindered, and their virulence factors were reduced, which ultimately lowered the abundance and pathogenicity of HBPs. Collectively, our study provides insights into the role of biochar in decreasing the risks of HBPs, which is significant in the development of biochar-based technologies for soil remediation.

Captivity increased the abundance of high-risk antibiotic resistance genes in the giant panda gut microbiome

Captivity is a key strategy for protecting endangered species, but research has primarily focused on artificial breeding and reintroduction to bolster wild populations, often overlooking the environmental and health risks associated with antibiotic resistance genes (ARGs). Here, we conducted a comprehensive analysis of the microbiome and ARG profiles in the gut of wild giant pandas across five representative populations, as well as one captive population, utilizing 16S rRNA gene sequencing and High-Throughput Quantitative PCR. Our findings revealed that both geographic location and captivity significantly influenced the gut microbial community and ARG composition in the gut of giant pandas. Additionally, we identified core microbiomes with essential ecological functions, particularly those related to food utilization, were identified in the giant panda gut across different regions. The gut ARGs in giant pandas exhibited a broad range of subtypes, with multidrug resistance genes being the most prevalent. Notably, the captive population harbored the highest abundance of high-risk ARGs, especially those conferring tetracycline resistance. High-risk multidrug ARGs (e.g., tolC, mepA, and mdtA) were found to be strongly correlated with the potential pathogens, such as Escherichia_Shigellina and Pseudomonas. Furthermore, bamboo-associated ARGs and mobile genetic elements (MGEs) contributed significantly to the ARG abundance in the giant panda gut, indicating that diet plays a crucial role in shaping gut resistome. Collectively, our study provides a detailed mapping of giant panda gut microbiomes and ARG distribution, offering valuable insights for conservation efforts and advancing our understanding of ARG dynamics in giant panda populations.

Recovery of intestinal microbial community in Penaeus vannamei after florfenicol perturbation

The concept and application of probiotic intervention for restoring intestinal microbial dysbiosis induced by antibiotics in aquaculture are still in early stages. This study aimed to investigate potential responses of various recovery strategies, including natural recovery and probiotic intervention, in restoring the growth and intestinal microbial community of Penaeus vannamei following florfenicol perturbation. The basal diet (control, CN) was supplemented with florfenicol (FC) or Lactobacillus plantarum W2 (LM) throughout the entire feeding trial. Meanwhile, the basal diet was supplemented with florfenicol for 7 days, followed by a period without florfenicol (natural recovery, FB), or with live strain W2 (probiotic recovery, FM), for a duration of 35 days. Results indicated that dietary supplementation of strain W2, whether continuous or following florfenicol perturbation, along with continuous florfenicol supplementation, significantly enhanced the growth performance of shrimp. Early natural recovery and probiotic intervention did not induce significant alterations in microbial diversity and community structure. Florfenicol perturbation resulted in a decrease in the abundance of potentially beneficial bacteria in intestinal microbial community of shrimp. However, both probiotic intervention and natural recovery strategies gradually reduced the abundance of potentially pathogenic bacteria while increasing the abundance of potentially beneficial ones. The robustness of microbial network decreased during florfenicol perturbation, showed gradual improvement during probiotic recovery, and remained relatively low during natural recovery and continuous florfenicol supplementation. Moreover, the microbial community composition in intestinal habitat significantly differed under various recovery strategies compared to the control. Notably, the microbial community composition of intestinal habitat following probiotic recovery exhibited greater similarity to that of continuous strain W2 supplementation without florfenicol perturbation. In summary, dietary supplementation of florfenicol perturbed intestinal microbial community stability of shrimp, whereas probiotic intervention and natural recovery facilitated the attainment of new stable states by altering keystone taxa. Considering intestinal microbial community stability of shrimp, the recovery of microbial community through probiotic intervention appears to be more effective than natural recovery.

Vertical migration and leaching behavior of antibiotic resistance genes in soil during rainfall: Impact by long-term fertilization

The vertical migration and leaching behavior of antibiotic resistance genes (ARGs) during rainfall in soils subjected to long-term fertilization remain largely unclear. In this study, ARGs in vertical profiles (0-60 cm) and leachates from three soils (acidic, neutral, and calcareous) in a long-term (13 years) field fertilization experiment were monitored by high-throughput quantitative PCR after each rainfall event throughout an entire year. The results showed that, compared with unfertilized soils, long-term manure fertilization mainly promoted the vertical migration and leaching of aminoglycoside, beta-lactam, and multidrug resistance genes in the soil profiles. As a result, the annual cumulative loads of ARGs in leachates from the three soils with long-term manure fertilization were significantly increased compared to the controls and were in the order of acidic soil > neutral soil > calcareous soil. SourceTracker analyses revealed that manured soil was the predominant source of the ARGs in the soil leachate samples. Pseudomonas, Anaeromyxobacter, IMCC26256, and MND1 were identified as the dominant potential hosts responsible for the vertical migration and leaching of ARGs in the three soils. PiecewiseSEM analysis further showed that long-term manure fertilization affected the vertical migration of ARGs during rainfall mainly by altering soil properties (i.e., pH, soil organic carbon, and sand). Our results suggest that the ARGs in soils with long-term manure fertilization are a significant potential source of ARG pollution in groundwater, and the measures should be taken to mitigate the vertical migration and leaching of ARGs during rainfall.

Pollution characteristics of heavy metals, antibiotic and antibiotic resistance genes in the crested ibis and their habitat across different lifestyle and geography

Antibacterial resistance in wild animals has been increasingly reported worldwide, even though they are usually not directly exposed to clinically relevant antibiotics. Crested ibis, one of the rarest birds in the world, usually forages in paddy fields and prefer to nest and breed near villages that is greatly influenced by anthropogenic activities. We sampled the feces of crested ibises, as well as their habitat environment samples, to explore the pollution characteristics of heavy metals, antibiotics and antibiotic resistance genes (ARGs). Results showed that the pollution characteristics of heavy metals, antibiotic, ARGs and gut microbiota of crested ibis were more related by host lifestyle and habitats. Captive ibises had higher relative abundances of the total ARGs and tetracycline concentrations compared with feralization and wild ibises, while the heavy metal contents had shown the opposite result. The Characteristics of pollutants in the corresponding environmental samples also exhibited high similarity with the results of fecal samples. The relative abundances of Proteobacteria and Actinobacteria were significantly different between captive and wild individuals, while the abundance of majority bacterial genera was generally higher in wild populations. The concentrations of heavy metals in soil (Cd, Cu and Zn) and water (Cd, Cu, Zn and Cr) were both exceeded the background soil levels or surface water quality standards, suggesting multi-element contamination in the habitat. Ecological risk assessments of soils by Igeo and Er showed that the habitats of wild ibises were heavily and moderately contaminated by Cd, which would possibly pose a threat to the health of ibises. PLS-PM analysis indicated that microbial compositions and residual antibiotics had the most substantial impact on the dynamic changes in ARGs of ibis. Overall, this work provides a comprehensive understanding of the characteristics, risks of those contaminations, and their effects on the ARGs in the habitat of crested ibis.

Assessment of health risk of antibiotics resistance genes from human disturbed habitat to wild animals: Metagenomic insights into availability and functional changes of gut microbiome

Not all antibiotic resistance genes (ARGs) pose an ecological risk to their host animals. A standard should be developed to study which types of ARGs posed an ecological risk to wild animals under human disturbances (HDs). In this study, the golden snub-nosed monkeys (Rhinopithecus roxellana) were used as sentinel species. According to the animals-associated enrichment, mobility, and pathogenicity, the ARGs in habitat of sentinel species were divided into four levels. If the mobile and pathogenic ARGs that could be collinear with the metagenome-assembled genome (MAGs) in the gut of the sentinel species, the ARGs were defined as Rank I ARGs and they were considered to have ecological risk to sentinel species. Functional genes in the MAGs that collinear with the Rank I ARGs were used to predict the health risks of sentinel species. The ecological risk to sentinel species was present in 0.158 % of the ARGs-contigs in the habitat. Cultivation and villages, but not grazing, agriculture and ecotourism, increased the ecological risk of the ARGs to wild animals, The ability of gut microbiome to acquire mobile and pathogenic ARGs increased, as did the collinear functional genes, and the health risks of the wild animals also enhanced by the disturbances of cultivation and villages. Cultivation and villages increased the nutrient content of the soil, and they had a positive effect on the ecological risk of Rank I ARGs by affecting the mobile genetic elements (MGEs), microbiome and the resistant group in the habitat, which was why the cultivation and villages increased the health risks of wild animals. We proposed that cultivation and living should be controlled, while grazing, agriculture and ecotourism could be developed in nature reserves of wild animals, but the nutrients in the wild animals' habitat should be monitored.

Antibiotics and Pesticides Enhancing the Transfer of Resistomes among Soil-Bayberry-Fruit Fly Food Chain in the Orchard Ecosystem

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

Ecological risk assessment of castor oil based waterborne polyurethane: Mechanism of anionic/cationic state selective toxicity to Eisenia fetida

Cationic and anionic castor oil-based waterborne polyurethanes (C-WPU/A and C-WPU/C) have great potential for development in agriculture. However, it is still unclear whether these polyurethanes are harmful or toxic to soil fauna. Based on multilevel toxicity endpoints and transcriptomics, we investigated the effects of C-WPU/A and C-WPU/C on earthworms (Eisenia fetida). The acute toxicity results showed that C-WPU/A was highly toxic to the earthworms, whereas C-WPU/C was nearly nontoxic. C-WPU/A significantly affected the body weight, burrowing ability and cocoon production rate of earthworms compared to C-WPU/C. After exposure to C-WPU/A, the results showed accumulation of reactive oxygen species (ROS), abnormal peroxidase activity, and increased malondialdehyde levels. Additionally, more serious histopathological damage was observed in earthworms, such as epidermal damage, vacuolization, longitudinal muscle disorganization, and shedding of intestinal epidermal cells. At the cellular level, C-WPU/A induced more severe lysosomal damage, DNA damage and apoptosis than C-WPU/A. C-WPU/A made more differentially expressed genes and considerably more enriched pathways at the transcriptional level than C-WPU/C. These pathways are largely involved in cell membrane signaling, detoxification, and apoptosis. These results provide an important reference for elucidating the selective toxicity mechanisms of C-WPU/A and C-WPU/C in earthworms.

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.

Impact of earthworms on antibiotic resistance genes removal in ampicillin-contaminated soil through bacterial community alteration

The emergence of antibiotic resistance genes (ARGs) as contaminants in soil poses a significant threat to public health. Earthworms (Eisenia foetida), which are common inhabitants of soil, have been extensively studied for their influence on ARGs. However, the specific impact of earthworms on penicillin-related ARGs remains unclear. In this study, we investigate the role of earthworms in mitigating ARGs, specifically penicillin-related ARGs, in ampicillin-contaminated soil. Utilizing high-throughput quantitative PCR (HT-qPCR), we quantified a significant reduction in the relative abundance of penicillin-related ARGs in soil treated with earthworms, showing a decrease with a p-value of <0.01. Furthermore, high-throughput 16S rRNA gene sequencing revealed that earthworm intervention markedly alters the microbial community structure, notably enhancing the prevalence of specific bacterial phyla such as Proteobacteria, Firmicutes, Chloroflexi, and Tenericutes. Our findings not only demonstrate the effectiveness of earthworms in reducing the environmental load of penicillin-related ARGs but also provide insight into the alteration of microbial communities as a potential mechanism. This research contributes to our understanding of the role of earthworms in mitigating the spread of antibiotic resistance and provides valuable insights for the development of strategies to combat this global health issue.

Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum

Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.