Deciphering Potential Roles of Earthworms in Mitigation of Antibiotic Resistance in the Soils from Diverse Ecosystems

Vermicompost: In situ retardant of antibiotic resistome accumulation in cropland soils

The dissemination of antibiotic resistance genes (ARGs) in soil has become a global environmental issue. Vermicomposting is gaining prominence in agricultural practices as a soil amendment to improve soil quality. However, its impact on soil ARGs remains unclear when it occurs in farmland. We comprehensively explored the evolution and fate of ARGs and their hosts in the field soil profiles under vermicompost application for more than 3 years. Vermicompost application increased several ARG loads in soil environment but decreased the high-risk bla-ARGs (blaampC, blaNDM, and blaGES-1) by log(0.04 - 0.43). ARGs in soil amended with vermicompost primarily occurred in topsoil (approximately 1.04-fold of unfertilized soil), but it is worth noting that their levels in the 40-60 cm soil layer were the same or even less than in the unfertilized soil. The microbial community structure changed in soil profiles after vermicompost application. Vermicompost application altered the microbial community structure in soil profiles, showing that the dominant bacteria (i.e., Proteobacteria, Actinobacteriota, Firmicutes) were decreased 2.62%-5.48% with the increase of soil depth. A network analysis further revealed that most of ARG dominant host bacteria did not migrate from surface soil to deep soil. In particular, those host bacteria harboring high-risk bla-ARGs were primarily concentrated in the surface soil. This study highlights a lower risk of the propagation of ARGs caused by vermicompost application and provides a novel approach to reduce and relieve the dissemination of ARGs derived from animals in agricultural production.

Dissemination of antimicrobial resistance in agricultural ecosystems following irrigation with treated municipal wastewater

The spread of antimicrobial resistance (AMR) in agricultural systems via irrigation water is a serious public health issue as it can be transmitted to humans through the food chain. Therefore, understanding the dissemination routes of antibiotic resistance genes (ARGs) in agricultural systems is crucial for the assessment of health risks associated with eating fresh vegetables such as spinach and radish irrigated with treated municipal wastewater (TMW). In this study, we investigated the bacterial community structure and resistome in the soil-plant-earthworm continuum after irrigation of spinach and radish with TMW containing the antibiotics trimethoprim (TMP), sulfamethoxazole (SMZ), and sulfapyridine (SPD) using 16S rRNA gene sequencing and high throughput quantitative PCR (HT-qPCR). The study was conducted in two phases: Phase I involved eight weeks of spinach and radish production using TMW for irrigation, whereas Phase II entailed three weeks of earthworm exposure to contaminated plant material obtained in Phase I. The 16S data indicated that the rhizosphere bacterial community composition and structure were more resilient to antibiotic residuals in the irrigated water, with radish showing less susceptibility than spinach than those of bulk soils. The HT-qPCR analysis revealed that a total of 271 ARGs (out of 285) and 9 mobile genetic elements (MGEs) (out of 10) were detected in all samples. Higher diversity and abundance of ARGs were observed for samples irrigated with higher concentrations of antibiotics in both spinach and radish treatments. However, compared to spinach, radish ARG dynamics in the soil biome were more stable due to the change of antibiotic introduction to the soil. At the class level, multi-drug resistance (MDR) class was altered significantly by the presence of antibiotics in irrigation water. Compared to earthworm fecal samples, their corresponding soil environments showed a higher number of detected ARGs, suggesting that earthworms could play a role in reducing ARG dissemination in the soil environments. These findings will not only provide insight into the dissemination of ARGs in agricultural environments due to antibiotic residuals in irrigated water but could help understand the potential human health risks associated with ARGs.

Comparative study of reactive oxygen species and tetracycline degradation pathways in catalytic peroxodisulfate activation by asymmetric mesoporous TiO2 and the corresponding controlled-release materials

The removal of trace amounts of antibiotics from water environments while simultaneously avoiding potential environmental hazards during the treatment is still a challenge. In this work, green, harmless, and novel asymmetric mesoporous TiO2 (A-mTiO2) was combined with peroxodisulfate (PDS) as active components in a controlled-release material (CRM) system for the degradation of tetracycline (TC) in the dark. The formation of reactive oxygen species (ROS) and the degradation pathways of TC during catalytic PDS activation by A-mTiO2 powder catalysts and the CRMs were thoroughly studied. Due to its asymmetric mesoporous structure, there were abundant Ti3+/Ti4+ couples and oxygen vacancies in A-mTiO2, resulting in excellent activity in the activation of PDS for TC degradation, with a mineralization rate of 78.6%. In CRMs, ROS could first form during PDS activation by A-mTiO2 and subsequently dissolve from the CRMs to degrade TC in groundwater. Due to the excellent performance and good stability of A-mTiO2, the resulting constructed CRMs could effectively degrade TC in simulated groundwater over a long period (more than 20 days). From electron paramagnetic resonance analysis and TC degradation experiments, it was interesting to find that the ROS formed during PDS activation by A-mTiO2 powder catalysts and CRMs were different, but the degradation pathways for TC were indeed similar in the two systems. In PDS activation by A-mTiO2, besides the free hydroxyl radical (·OH), singlet oxygen (1O2) worked as a major ROS participating in TC degradation. For CRMs, the immobilization of A-mTiO2 inside CRMs made it difficult to capture superoxide radicals (·O2-), and continuously generate 1O2. In addition, the formation of sulfate radicals (·SO4-), and ·OH during the release process of CRMs was consistent with PDS activation by the A-mTiO2 powder catalyst. The eco-friendly CRMs had a promising potential for practical application in the remediation of organic pollutants from groundwater.

Exploring the Toxicity of Oxytetracycline in Earthworms (Eisenia fetida) Based on the Integrated Biomarker Response Method

Antibiotic contamination has become a global environmental issue of widespread concern, among which oxytetracycline contamination is very severe. In this study, earthworm (Eisenia fetida) was exposed to oxytetracycline to study its impact on the soil environment. The total protein (TP), catalase (CAT), superoxide dismutase (SOD), peroxidase (POD), malondialdehyde (MDA), glutathione S-transferase (GST), and glutathione peroxidase (GPX) oxidative stress indicators in earthworms were measured, and the integrated biomarker response (IBR) approach was used to evaluate the toxic effect of oxytetracycline on earthworms. A Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS) and a path analysis model were used to explore the physiological and metabolic processes of earthworms after stress occurs. The results showed that SOD, GPX, and GST play important roles in resisting oxytetracycline stress. In addition, stress injury showed a good dose-effect relationship, and long-term stress from pollutants resulted in the most serious damage to the head tissue of earthworms. These results provide a theoretical basis for understanding the toxic effect of oxytetracycline on soil animals, monitoring the pollution status of oxytetracycline in soil, and conducting ecological security risk assessment.

Soil health hazards of di(2-ethylhexyl) phthalate: New perspectives on earthworms from different ecological niches DNA damage, gut microbial disruption and soil enzyme changes

Di(2-ethylhexyl) phthalate (DEHP) is perceived an emerging threat to terrestrial ecosystem, however, clear and accurate studies to fully understander ecotoxicity and underlying mechanisms of DEHP on the soil fauna remain poorly understood. Therefore, this study conducted a microcosm experiment of two earthworm ecotypes to investigate the ecological hazards of DHEP from multiple perspectives. The results showed that DEHP significantly increased the 8-hydroxy-deoxyguanosine (8-OHdG) content both in Eisenia foetida (13.76-133.0%) and Metaphire guillelmi (11.01-49.12%), leading to intracellular DNA damage. Meanwhile, DEHP negatively affected the expression of functional genes (ATP-6, NADH1, COX), which may be detrimental to mitochondrial respiration and oxidative stress at the gene level. The two earthworm guts shared analogous dominant bacteria however, the incorporation of DEHP drastically suppressed the homogeneity and diversity of the gut microbes, which further disrupted the homeostasis of the gut microbial ecological network. The keystone species in the gut of E. foetida decreased under DEHP stress but increased in the gut of M. guillelmi. Moreover, DEHP presented detrimental effects on soil enzyme activity, which is mainly associated with pollutant levels and earthworm activity. Collectively, the findings expand the understanding of soil ecological health and reveal the underlying mechanisms of the potential exposure risk to DEHP.

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.

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.

Effects of heavy metal and disinfectant on antibiotic resistance genes and virulence factor genes in the plastisphere from diverse soil ecosystems

Antibiotic-resistance genes (ARGs) are world-wide contaminants posing potential health risks. Quaternary ammonium compounds (QACs) and heavy metals can apply selective pressure on antibiotic resistance. However, there is a lack of evidence regarding their coupled effect on changes in ARGs and virulence factor genes (VFGs) in various soil types and their plastispheres. Herein, we conducted a microcosm experiment to explore the abundances and profiles of ARGs and VFGs in soil plastispheres from three distinct types of soils amended with Cu and disinfectants. The plastispheres enriched the ARGs' abundance compared to soils and stimulated the coupling effect of combined pollutants on promoting the abundances of ARGs and VFGs. Horizontal gene transfer inevitably accelerates the propagation of ARGs and VFGs in plastispheres under pollutant stress. In plastispheres, combined exposure to disinfectants and Cu increased some potential pathogens' relative abundances. Moreover, the combined effect of disinfectants and Cu on ARGs and VFGs changed with soil type in plastispheres, emphasising the necessity to incorporate soil type considerations into health risk assessments for ARGs and VFGs. Overall, this study highlights the high health risks of ARGs under the selective pressure of combined pollutants in plastispheres and provides valuable insights for future risk assessments related to antibiotic resistance.

Characterization of a blaNDM-1-positive Citrobacter freundii strain isolated from earthworms

OBJECTIVES

Earthworms are one of the key components of soil, and they play a crucial role in the transformation of various nutrients and pollutants in the soil. The purpose of this study is to characterize the NDM-1-producing C. freundii isolated from soil-dwelling earthworms near a hospital, exploring their potential role as carriers of carbapenem-resistant genes.

METHODS

Isolates were isolated from the intestines of earthworms and identified by MALDI-TOF MS. The presence of NDM enzyme was verified through the CARBA-5 Assay. Whole genome sequencing was conducted using the Illumina NovaSeq PE150 platform. Antimicrobial susceptibility testing and conjugation experiment were performed for phenotypic analysis.

RESULTS

This isolate exhibited a multidrug-resistant profile, including resistance to imipenem, meropenem, and ertapenem and successfully transferred blaNDM-1 gene to Escherichia coli. Whole genomic sequencing showed that blaNDM-1 gene was located on an IncFIIY-type plasmid. Phylogenetic analysis revealed a close relationship between the QY221001 strain obtained from earthworms and the human isolate F2021 in the NCBI database, both of which were collected in Hangzhou, China.

CONCLUSION

To our knowledge, this is the first report of an NDM-1-producing bacteria isolated from the intestine of an earthworm. Our finding suggested that earthworms could be a potential reservoir of carbapenem resistance genes, emphasizing the importance of enhanced environmental monitoring of antimicrobial resistance.

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.

Co-exposure to UV-aged microplastics and cadmium induces intestinal toxicity and metabolic responses in earthworms

Aged microplastics (MPs) alter the interaction with heavy metals due to changes in surface properties. However, the combined toxicological effects of aged MPs on heavy metals in soil remain poorly understood. In this study, earthworms were employed as model animals to investigate the effects of aged MPs on the biotoxicity of cadmium (Cd) by simulating the exposure patterns of original and UV-aged MPs (polylactic acid (PLA) and polyethylene (PE)) with Cd. The results showed that UV-aging decreased the zeta potential and increased the specific surface area of the MPs, which enhanced the bioaccumulation of Cd and caused more severe oxidative stress to earthworms. Meanwhile, the earthworm intestines exhibited increased tissue damage, including chloragogenous tissue congestion lesions, and typhlosole damage. Furthermore, the combined exposure to UV-aged MPs and Cd enhanced the complexity of the microbial network in the earthworm gut and interfered with endocrine disruption, membrane structure, and energy metabolic pathways in earthworms. The results emphasized the need to consider the degradation of MPs in the environment. Hence, we recommend that future toxicological studies use aged MPs that are more representative of the actual environmental conditions, with the results being important for the risk assessment and management of MPs.

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.

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

Recently, the study of antibiotic resistance in the soil animal microbiome has attracted extensive attention; however, the patterns of antibiotic resistance genes (ARGs) in soil and soil animals related to different land use types remain poorly studied. In the present study, soil and earthworms were collected from four different land-use types (farmland, hospital, park land, and mountain park), and 162 ARGs in the microbiomes of the soil and earthworms were quantified using high-throughput quantitative PCR. Our study showed that the abundance and number of ARGs were higher in soil samples than in earthworm guts, but earthworms as the living organisms created relatively isolated ambient surroundings, which allowed for a more heterogeneous ARGs profile. Meanwhile, land use significantly influenced the abundance, number and co-occurrence pattern of ARGs in the soil and earthworm samples. Furthermore, abiotic and biotic factors had significant effects on the ARGs profile, among which pH had a negative effect on the ARGs profiles of both soil and earthworm microbiomes, and bacterial network complexity had a positive effect on the earthworm ARGs profile. Our study provides new insights into the distribution and dispersal of ARGs in the soil animal gut microbiome under different land use patterns.

Dissemination of antibiotic resistance genes through soil-plant-earthworm continuum in the food production environment

Treated municipal wastewater (TMW) can provide a reliable source of irrigation water for crops, which is especially important in arid areas where water resources are limited or prone to drought. Nonetheless, TMW may contain residual antibiotics, potentially exposing the crops to these substances. The goal of this study was to investigate the dissemination of antibiotics resistance genes (ARGs) in the soil-plant-earthworm continuum after irrigation of spinach and radish plants with TMW containing trimethoprim, sulfamethoxazole, and sulfapyridine in a greenhouse experiment, followed by feeding of earthworms with harvested plant materials. Our results showed that antibiotic resistance genes (ARGs) were enriched in the soil-plant-earthworm microbiomes irrigated with TMW and TMW spiked with higher concentrations of antibiotics. The number of ARGs and antibiotic-resistant bacteria (ARB) enrichment varied with plant type, with spinach harboring a significantly higher amount of ARGs and ARB compared to radish. Our data showed that bulk and rhizosphere soils of spinach and radish plants irrigated with MilliQ water, TMW, TMW10, or TMW100 had significant differences in bacterial community (p < 0.001), ARG (p < 0.001), and virulence factor gene (VFG) (p < 0.001) diversities. The abundance of ARGs significantly decreased from bulk soil to rhizosphere to phyllosphere and endosphere. Using metagenome assembled genomes (MAGs), we recovered many bacterial MAGs and a near complete genome (>90 %) of bacterial MAG of genus Leclercia adecarboxylata B from the fecal microbiome of earthworm that was fed harvested radish tubers and spinach leaves grown on TMW10 irrigated waters, and this bacterium has been shown to be an emerging pathogen causing infection in immunocompromised patients that may lead to health complications and death. Therefore, crops irrigated with TMW containing residual antibiotics and ARGs may lead to increased incidences of enrichment of ARB in the soil-plant-earthworm continuum.

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.

Responses of soil and collembolan (Folsomia candida) gut microbiomes to 6PPD-Q pollution

The potential risk of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-Q) to soil organisms remains poorly understood. Here we showed that 6PPD-Q pollution inhibited the survival of collembolans (Folsomia candida) with the chronic median lethal concentration (LC50) of 16.31 μg kg-1 in a 28-day soil culture. The microbe-microbe interactions between abundant taxa in soil and collembolan gut helped alleviate the negative impact of 6PPD-Q on soil microbial community, while rare taxa contributed to maintaining microbial network complexity and stability under 6PPD-Q stresses. Gammaproteobacteria, Alphaproteobacteria and Actinobacteria in the gut of both adult and juvenile collembolans were identified as potential indicators for 6PPD-Q exposure. Such responses were accompanied by increases in the relative abundances of genes involved in nutrient cycles and their interactions between soil and collembolan gut microbiomes, which enhanced nitrogen and carbon turnover in 6PPD-Q polluted soil, potentially alleviating the stresses caused by 6PPD-Q. Overall, this study sheds new light on the toxicity of 6PPD-Q to soil organisms and links 6PPD-Q stresses to microbial responses and soil functions, thus highlighting the urgency of assessing its potential risk to the terrestrial ecosystem.

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.

Nematodes Degrade Extracellular Antibiotic Resistance Genes by Secreting DNase II Encoded by the nuc-1 Gene

This study investigated the degradation performance and mechanism of extracellular antibiotic resistance genes (eARGs) by nematodes using batch degradation experiments, mutant strain validation, and phylogenetic tree construction. Caenorhabditis elegans, a representative nematode, effectively degraded approximately 99.999% of eARGs (tetM and kan) in 84 h and completely deactivated them within a few hours. Deoxyribonuclease (DNase) II encoded by nuc-1 in the excretory and secretory products of nematodes was the primary mechanism. A neighbor-joining phylogenetic tree indicated the widespread presence of homologs of the NUC-1 protein in other nematodes, such as Caenorhabditis remanei and Caenorhabditis brenneri, whose capabilities of degrading eARGs were then experimentally confirmed. C. elegans remained effective in degrading eARGs under the effects of natural organic matter (5, 10, and 20 mg/L, 5.26-6.22 log degradation), cation (2.0 mM Mg2+ and 2.5 mM Ca2+, 5.02-5.04 log degradation), temperature conditions (1, 20, and 30 °C, 1.21-5.26 log degradation), and in surface water and wastewater samples (4.78 and 3.23 log degradation, respectively). These findings highlight the pervasive but neglected role of nematodes in the natural decay of eARGs and provide novel approaches for antimicrobial resistance mitigation biotechnology by introducing nematodes to wastewater, sludge, and biosolids.

Mitigation effects and microbial mechanism of two ecological earthworms on the uptake of chlortetracycline and antibiotic resistance genes in lettuce

The contamination of greenhouse vegetable soils with antibiotics and antibiotic resistance genes (ARGs), caused by the application of livestock and poultry manure, is a prominent environmental problem. In this study, the effects of two ecological earthworms (endogeic Metaphire guillelmi and epigeic Eisenia fetida) on the accumulation and transfer of chlortetracycline (CTC) and ARGs in a soil-lettuce system were studied via pot experiments. The results revealed that earthworm application accelerated the removal of the CTC from the soil and lettuce roots and leaves, with the CTC content reducing by 11.7-22.8 %, 15.7-36.1 %, and 8.93-19.6 % compared with that of the control, respectively. Both earthworms significantly reduced the CTC uptake by lettuce roots from the soil (P < 0.05) but did not change the CTC transfer efficiency from the roots to leaves. The high-throughput quantitative PCR results showed that the relative abundance of ARGs in the soil and lettuce roots and leaves decreased by 22.4-27.0 %, 25.1-44.1 %, and 24.4-25.4 %, respectively, with the application of earthworms. Earthworm addition decreased the interspecific bacterial interactions and the relative abundance of mobile genetic elements (MGEs), which helped reduce the dissemination of ARGs. Furthermore, some indigenous soil antibiotic degraders (Pseudomonas, Flavobacterium, Sphingobium, and Microbacterium) were stimulated by the earthworms. The results of redundancy analysis indicated that the bacterial community composition, CTC residues, and MGEs were the main parameters affecting the distribution of ARGs, accounting for 91.1 % of the total distribution. In addition, the bacterial function prediction results showed that the addition of earthworms reduced the abundance of some pathogenic bacteria in the system. Overall, our findings imply that earthworm application can substantially reduce the accumulation and transmission risk of antibiotics and ARGs in soil-lettuce systems, providing a cost-effective soil bioremediation practice for addressing antibiotic and ARGs contamination to guarantee the safety of vegetables and human health.

Antibiotic resistomes in face-mask biofilm along an urban river: Multiple drivers and co-occurrence with human opportunistic pathogens

Discarded face masks from the global COVID-19 pandemic have contributed significantly to plastic pollution in surface water, whereas their potential as a reservoir for aquatic pollutants is not well understood. Herein, we conducted a field experiment along a human-impacted urban river, investigating the variations of antibiotic resistance genes (ARGs), pathogens, and water-borne contaminants in commonly-used face masks. Results showed that high-biomass biofilms formed on face masks selectively enriched more ARGs than stone biofilm (0.08-0.22 vs 0.07-0.15 copies/16 S rRNA gene copies) from bulk water, which mainly due to unique microbial communities, enhanced horizontal gene transfer, and selective pressure of accumulated contaminants based on redundancy analysis and variation partitioning analysis. Several human opportunistic pathogens (e.g., Acinetobacter, Escherichia-Shigella, Bacillus, and Klebsiella), which are considered potential ARG carriers, were also greatly concentrated in face-mask biofilms, imposing a potential threat to aquatic ecological environment and human health. Moreover, wastewater treatment plant effluents, as an important source of pollutants to urban rivers, further aggravated the abundances of ARGs and opportunistic pathogens in face-mask biofilms. Our findings demonstrated that discarded face masks provide a hotspot for the proliferation and spread of ARGs and pathogens in urban water, highlighting the urgent requirement for implementing stricter regulations in face mask disposal.

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.

Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus

Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.

Deciphering roles of microbiota in arsenic biotransformation from the earthworm gut and skin

Biotransformation mediated by microbes can affect the biogeochemical cycle of arsenic. However, arsenic biotransformation mediated by earthworm-related microorganisms has not been well explored, especially the role played by earthworm skin microbiota. Herein, we reveal the profiles of arsenic biotransformation genes (ABGs) and elucidate the microbial communities of the earthworm gut, skin, and surrounding soil from five different soil environments in China. The relative abundance of ABGs in the earthworm skin microbiota, which were dominated by genes associated with arsenate reduction and transport, was approximately three times higher than that in the surrounding soil and earthworm gut microbiota. The composition and diversity of earthworm skin microbiota differed significantly from those of the soil and earthworm gut, comprising a core bacterial community with a relative abundance of 96% Firmicutes and a fungal community with relative abundances of 50% Ascomycota and 13% Mucoromycota. In addition, stochastic processes mainly contributed to the microbial community assembly across all samples. Moreover, fungal genera such as Vishniacozyma and Oomyces were important mediators of ABGs involved in the biogeochemical cycle of arsenic. This is the first study to investigate earthworm skin as a reservoir of microbial diversity in arsenic biotransformation. Our findings broaden the current scientific knowledge of the involvement of earthworms in the arsenic biogeochemical cycle.

Animal manure as a biostimulant in bioremediation of oil-contaminated soil: the role of earthworms

Human dire need for environmental sustainability have triggered researchers to seek for organic substrates as an alternative to synthetic fertilizers in order to enhance bioremediation. Presently, nitrogen-rich organic substrate not only proffered the solution but also have proven useful in enhancing the rate of bioremediation. Animal manure is a nitrogen-rich organic substrate which has been found very effective for stimulating plant growth. Some of the animal manure used by researchers are poultry droppings, cow dung, goat manure, and pig manure. In all the papers reviewed, it was gathered that animal manure enhances bioremediation by providing nutrients favoring microbial growth and activities responsible hydrocarbon degradation. However, of the four commonly used animal manure, poultry droppings was severally reported to be a better biostimulant. Also, animal manure when sun-dried and pulverized yielded better results. It was observed that animal manure serves as substrates for earthworms which further accelerates the potential of the earthworms to remediate the soil. Also, the pollution of soil by crude oil causes a surge in its carbon content which may slow down microbial growth and activities. Thorough review of literatures, however, indicates that animal manure is capable of providing appropriate nutrient concentrations to offset such imbalance. Studies continue to lay credence to the efficacy of animal manure in enhancing microbial growth and activities responsible for the biodegradation of hydrocarbons contained in crude oil. Furthermore, the co-application of animal manure with other bioremediation strategies, such as phytoremediation and vermiremediation, should be combined for effective bioremediation of oil-contaminated environment.

Biotransformation kinetics and pathways of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) and its hydroxylated and methoxylated derivatives (6-OH-BDE-47 and 6-MeO-BDE-47) in earthworms (Eisenia fetida)

As a class of persistent organic pollutant, polybrominated diphenyl ethers (PBDEs) and their hydroxylated and methoxylated derivatives (OH-PBDEs and MeO-PBDEs) have been widely detected in soil environments. However, studies on the bioavailability and transformation of PBDEs and their derivatives in soil organisms remain scarce. In this study, a detailed kinetic investigation on the accumulation and biotransformations of BDE-47, 6-MeO-BDE-47 and 6-OH-BDE-47 in earthworms (Eisenia fetida) exposed to artificially contaminated soils was conducted. The uptake and elimination kinetics of BDE-47, 6-MeO-BDE-47 and 6-OH-BDE-47 by earthworms were in accordance with a one-compartment first-order kinetic model. The bioaccumulation factors (BAFs) followed the order 6-MeO-BDE-47 > 6-OH-BDE-47 > BDE-47. All three compounds could undergo step-by-step debromination to produce lower brominated analogs in earthworms. Both BDE-47 and 6-OH-BDE-47 could be transformed to MeO-PBDEs, whereas no transformation from 6-OH-BDE-47 or 6-MeO-BDE-47 to PBDEs or from BDE-47 and 6-MeO-BDE-47 to OH-PBDEs took place in the earthworms. Methoxylation was proposed as a potential metabolic pathway to form MeO-PBDEs in earthworms, with the metabolic rates for the methoxylation of BDE-47 and 6-OH-BDE-47 being 27.7 and 5.1 times greater, respectively, than that of the debromination metabolism. The isomers of 6-MeO-BDE-47 and 6-OH-BDE-47 were formed via the addition of methoxy/hydroxy groups or via bromine shifts on benzene ring in the earthworms. This study provides comprehensive information for a better understanding of the accumulation and biotransformation of PBDEs and their derivatives in earthworms.

Metagenomic and viromic analysis reveal the anthropogenic impacts on the plasmid and phage borne transferable resistome in soil

Anthropogenic land use changes have been recognized with significant effects on the abundance and diversity of antibiotic resistance genes (ARGs) in soil, but their impacts on ARGs with potential health risk remained poorly understood. In this study, paired metagenomes and viromes were obtained from soils (Anthrosols and Nitisols) with different land uses including urban parks, road verge, forests, vegetable and paddy in a subtropical city, Xiamen, and soils (Anthrosols) with various long-term fertilization treatments in Dezhou located in temperate region, respectively, to explore the influence of anthropogenic activity on soil resistome. The diversity and abundance of antibiotic resistance genes (ARGs) were profiled, and the risk associated factors of ARGs, i.e., genetic location, host, and co-existence with virulence factors (VFs), were systematically investigated at reads and contigs level. We observed that agricultural areas significantly enriched human-related ARGs and viruses, and positively related with clinical ARGs. Most of the ARG-carrying contigs were chromosomes (∼85 %), while, human-related ARGs presented a higher odds ratio to locate on plasmids. Soil VFs exhibited land use pattern and distinct distribution between chromosome and plasmids, but less mobile than ARGs. Analysis of 131,014 soil viral genomes indicated that they barely encoded ARGs, nevertheless, transduction of VLPs was implicated in the spread of ARGs. The results can be mutually verified in Xiamen and Dezhou datasets. Overall, the agricultural soils with dry-farming are hotspots for the clinical ARGs, and the transmission of clinical ARGs between human dominated environments and soil is primarily mediated by plasmids, rather than bacterial chromosomes, and the transduction of human-gut related viruses could participate the process. These results highlight the importance of tracking the fate of clinical ARGs for better evaluating the impacts of human activities on soil resistome.

Does Plant Identity Affect the Dispersal of Resistomes Above and Below Ground?

Resistomes are ubiquitous in natural environments. Previous studies have shown that both the plant phyllosphere and soil-borne nematodes were reservoirs of above- and below-ground resistomes, respectively. However, the influence of plant identity on soil, nematode, and phyllosphere resistomes remains unclear. Here, a microcosm experiment was used to explore the characteristics of bacterial communities and resistomes in soil, nematode, and phyllosphere associated with six different plant identities (Lactuca sativa, Cichorium endivia, Allium fistulosum, Coriandrum sativum, Raphanus sativus, and Mesembryanthemum crystallinum). A total of 222 antibiotic resistance genes (ARGs) and 7 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR from all samples. Plant identity not only significantly affected the diversity of resistomes in soil, nematode, and phyllosphere but also influenced the abundance of resistomes in nematodes. Shared bacteria and resistomes indicated a possible pathway of resistomes transfer through the soil-nematode-phyllosphere system. Structural equation models revealed that plant identity had no direct effect on phyllosphere ARGs, but altered indirectly through complex above- and below-ground interactions (soil-plant-nematode trophic transfer). Results also showed that bacteria and MGEs were key factors driving the above- and below-ground flow of resistomes. The study extends our knowledge about the top-down and bottom-up dispersal patterns of resistomes.

Effects of Trophic Level and Land Use on the Variation of Animal Antibiotic Resistome in the Soil Food Web

In recent years, it has been increasingly recognized that soil animals are hidden reservoirs of antibiotic resistance genes (ARGs) and play a vital role in spreading ARGs in soil ecosystems. However, little is known about the variation of ARGs among different animals in the soil food web and effects of trophic levels and land uses on them. We characterized the antibiotic resistomes of 495 soil animal samples collected from six regions across China, including two different land uses. A total of 265 ARGs were detected in all animal samples, and relative abundances of ARGs in animals were significantly higher than in soils. In addition, significant differences in ARGs were observed among different animal groups. Twelve common ARGs were identified among all animal groups, accounting for 17.4% of total ARGs abundance. A positive and significant correlation was found between δ¹⁵N values (trophic level) and total ARGs abundance in animals. The relative abundance of ARGs in the soil food web from arable land was higher than forest land. Changes in soil antibiotics may indirectly affect animal resistome by altering soil ARGs. This study suggests that the risk of ARGs spreading through the food web is greater in arable than in forest ecosystems.

Indigenous earthworms and gut bacteria are superior to chemical amendments in the remediation of cadmium-contaminated seleniferous soils

The natural selenium (Se)-rich areas in China are generally characterized by high geological background of cadmium (Cd) which poses potential risks to human health. Therefore, immobilization of Cd is the prerequisite to ensure the safe utilization of natural seleniferous soil resources. A pot experiment was conducted to compare the effects of indigenous earthworm (Amynthas hupeiensis) and its gut bacteria (Citrobacter freundii DS strain) on the remediation of Cd-contaminated seleniferous soil with two traditional chemical amendments. The results indicated that earthworms and DS strain decreased DGT-extractable Cd by 25.52 - 41.53% and reduced Cd accumulation in lettuce leaves by 20.83 - 37.50% compared with control through converting the exchangeable Cd (EX-Cd) into residual Cd (RE-Cd) fractions. Overall, earthworms and DS strain were more effective in Cd immobilization, growth and quality promotion, oxidative stress alleviation, Cd accumulation and bioaccessibility reduction in the soil-lettuce-human continuum than biochar and lime. Moreover, all amendments induced the antagonism between Se and Cd through increasing bioavailable Se/Cd molar ratios in soil. However, all the Cd concentrations in lettuce exceeded the maximum permissible limit of Cd for leaf vegetables, indicating that soil amendment alone could not ensure food safety. This study confirmed that biological amendments were superior to chemical amendments in the remediation of Cd-contaminated seleniferous soil.

Dispersal of antibiotic resistance genes in an agricultural influenced multi-branch river network

Rivers in agricultural regions serve as an important sink for livestock and poultry farm runoff, fertilizer runoff, and country living sewage, which could bring antibiotic resistance genes (ARGs) contaminations. However, the diversity and distribution of ARGs has not been well documented in the agricultural influenced river. Here, the diversity of ARGs, and their relationship with biochemical factors were determined in the surface water in an agricultural region of the Jialing River and its five rural branches. The 218 unique ARGs encoding resistance to eight major antibiotic classes have been detected using high-throughput quantitative PCR. The branches of the river had a remarkably higher abundance of ARGs than the mainstream. The aminoglycoside, beta_Lactamase, MLSB, and Multidrug resistance genes were significantly enriched in the branches compared to the mainstream. Compared with the mainstream, the ARGs profiles in the branches showed obvious higher spatial variability. Significant correlation between ARGs profiles and bacterial community structures were observed, and network analysis further showed that the ARGs were associated with their potential hosts, such as Ottowia and Novosphingobium. Redundancy discrimination analysis revealed that Cu content has a significant contribution to the increase of ARGs in the river. The microbial diversity index was negatively correlated with the abundance of the ARGs. These results provide evidence for the enrichment of ARGs in the agricultural influenced river and branches due to the joint influence of chemical and microbial variables.

Quantitative relationship between earthworms' sensitivity to organic pollutants and the contaminants' degradation in soil: A meta-analysis

Using earthworms to remove soil organic pollutants is a common bioremediation method. However, it remains challenging to evaluate and predict their effect on removing soil organic pollutants based on earthworm toxicology and pollutant degradation rates. Peer-reviewed journal articles on ecotoxicology and bioremediation from the years 1974-2020 (cutoff date September 2020) were selected for meta-analysis to quantify the effect size of earthworms on organic pollutant degradation. The meta-analysis shows that the average effect size of earthworms on organic pollutant degradation is 128.5% (p < 0.05). Soils with high soil organic matter or clay textures are more conducive to earthworm-mediated removal of organic pollutants. Structural equation modeling reveals that earthworms' sensitivity to contaminant exposure may be a greater limiting factor on pollutant degradation than environmental factors. In addition, the quantitative relationship existed between LC50 and the pollutants' degradation that an elevated LC50 threshold resulted in at least 1.5 times increase in the pollutants' degradation size. This correlation was dually confirmed via meta-analysis and the validation trial. The results of this study contribute to a more profound understanding of the potential to use earthworms to mitigate organic pollution in soils and develop earthworm-based soil remediation techniques on a global scale.

Earthworms reduce the dissemination potential of antibiotic resistance genes by changing bacterial co-occurrence patterns in soil

Globally distributed earthworms affect compositions of soil compounds, microbial community structures, as well as antibiotic resistance genes (ARGs). Compared to their surroundings, earthworm gut is a simpler environment which could filter out microbes when soil passes through it. However, little is known about how earthworms affect the dissemination of ARGs in soil, and the understanding of the relationship between microbe-microbe interactions and ARGs is still lacking. Here, we designed a microcosm experiment with earthworm addition, and determined bacterial and fungal community compositions based on amplicon sequencing. We also examined mobile genetic elements (MGEs) and ARGs in earthworm gut and soils using high-throughput qPCR. The results showed significant differences of bacterial, fungal and ARG patterns between gut and soil. Earthworms indirectly impacted the patterns of ARGs in soils by affecting bacterial communities and soil properties, which play key roles in the distribution of ARGs and MGEs. The absolute abundances of MGEs in earthworm gut were significantly lower than those in soils, and earthworms reduce the absolute abundance of MGEs in soils. Earthworms changed the microbial co-occurrence patterns, and reduced bacterial connectivity, which were significantly and positively correlated with MGE abundance. These results highlight the importance of earthworm on the distribution and dissemination of ARGs in soils.

The ecological clusters of soil organisms drive the ecosystem multifunctionality under long-term fertilization

Long-term fertilization is known to impact the biodiversity and community structures of soil organisms, which are responsible for multiple soil ecosystem functions (multifunctionality). However the relationship between the alterations of soil organisms and ecosystem multifunctionality remains unclear, especially in the case of long-term fertilization. To explore the contribution of soil organismal biodiversity and community structures to ecosystem multifunctionality, we took soil samples from a nearly 25-year field fertilization experiment. Organic matter significantly improved the soil ecosystem multifunctionality. Ecosystem multifunctionality was found to be closely linked to the biodiversity and communities of soil organisms within the major ecological clustering of soil organisms (Module 1) according to the trophic co-occurrence network, rather than the entire community of soil organisms. This indicated that ecological clusters of soil organisms within the network were critical in maintaining soil ecosystem multifunctionality. The application of organic fertilization could enrich specialized soil organisms and increase interactions of soil organisms in the ecological cluster. As a result, our findings emphasize the role of ecological clusters in the soil organismal co-occurrence network in controlling soil multifunctionality after long-term fertilization, presenting a novel perspective on the link between soil biodiversity and ecosystem multifunctionality.

Responses of earthworm Metaphire vulgaris gut microbiota to arsenic and nanoplastics contamination

The growing contamination of arsenic and plastics has severely effects on the soil fauna health, including shifts of gut microbiota community. A few studies have focused on effects of microplastics and metal(loid) in soil and fauna gut microbiome. However, the environmental effect of nanoplastics and arsenic on the earthworm gut microbiota, especially on arsenic biotransformation in the gut, remain largely unknown. Here, a microcosm study was performed to explore the effects of nanoplastics and arsenic on the microbiota characteristics in earthworm Metaphire vulgaris gut using Illumina high throughput sequencing, and to investigate changes in the gut microbiota-mediated arsenic biotransformation genes (ABGs) by using high-throughput quantitative PCR. Our results demonstrated that the concentration of arsenic in the earthworm body tissues after exposure to arsenic and nanoplastics was significantly lower from that with arsenic alone exposure. Moreover, the clearly different bacterial community was observed in the soil compared with the earthworm gut, which was dominated by Proteobacteria, Actinobacteria, and Firmicutes at phylum level. Arsenic exposure significantly disturbed bacterial community structure in the earthworm gut, but exposure to nanoplastics did not induce gut microbiota changes. More interestingly, nanoplastics can relieve adverse effect of arsenic on the gut microbiota possibly by adsorbing arsenic. In addition, a total of 16 ABGs were detected, and predominant genes involved in arsenic reduction and transport process were observed in the earthworm guts. In short, this study provides a new picture of the effects of nanoplastics and arsenic on the gut microbiota and arsenic biotransformation in soil fauna gut.

Soil plastispheres as hotpots of antibiotic resistance genes and potential pathogens

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

Incubation trial indicated the earthworm intestinal bacteria as promising biodigestor for mitigating tetracycline resistance risk in anthropogenic disturbed forest soil

The continuous input of antibiotics due to frequent anthropogenic activities have increased the dissemination risk of antibiotic resistance genes (ARGs) in forest soil. As soil engineers, it remains unclear whether earthworm intestinal microbial communities might play a role in controlling the ARG proliferation in forest soil. This study collected forest soil in the Yangtze River Delta, China, and its resident Metaphire guillelmi to investigate the interaction between tetracycline (50 μg kg^-1) and the bacteria in worm gut and soil. Metagenome sequencing analysis indicated that the abundance of the total ARGs in both the soil (S2) and the worm gut (E2) was 1.3 (p < 0.001) and 1.2 (p < 0.001) times higher than the soil (S1) and (E1) without tetracycline exposure; and under tetracycline stress, the relative abundance of 36 and 20 bacterial genera in forest soil and worm gut were significantly increased respectively. However, the ARGs/ARB abundance decreased in the soil with the worm addition than that without, which may be related to the fact that earthworm intestinal bacteria harbored more tetracycline-degrading genes, i.e. dehydrogenase genes adh, ETFDH, and gpr, etc. Structural equation model analysis indicated that bacteria in worm intestinal has stronger ability to degrade tetracycline than in soil, and the main dissipate way was dehydrogenation. Together, the results contributed to understanding the promising role of worm intestinal bacteria in controlling the ARG risk caused by antibiotic disturbed forest soil.

Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants

BACKGROUND

The ubiquitous gut microbiotas acquired from the environment contribute to host health. The gut microbiotas of soil invertebrates are gradually assembled from the microecological region of the soil ecosystem which they inhabit, but little is known about their characteristics when the hosts are under environmental stress. The rapid development of high-throughput DNA sequencing in the last decade has provided unprecedented insights and opportunities to characterize the gut microbiotas of soil invertebrates. Here, we characterized the core, transient, and rare bacterial taxa in the guts of soil invertebrates using the core index (CI) and developed a new theory of global microbial diversity of soil ecological microregions.

RESULTS

We found that the Gammaproteobacteria could respond indiscriminately to the exposure to environmental concentrations of soil pollutants and were closely associated with the physiology and function of the host. Meanwhile, machine-learning models based on metadata calculated that Gammaproteobacteria were the core bacteria with the highest colonization potential in the gut, and further identified that they were the best indicator taxon of the response to environmental concentrations of soil pollution. Gammaproteobacteria also closely correlated with the abundance of antibiotic resistance genes.

CONCLUSIONS

Our results determined that Gammaproteobacteria were an indicator taxon in the guts of the soil invertebrates that responded to environmental concentrations of soil pollutants, thus providing an effective theoretical basis for subsequent assessments of soil ecological risk. The results of the physiological and biochemical analyses of the host and the microbial-community functions, and the antibiotic resistance of Gammaproteobacteria, provide new insights for evaluating global soil ecological health. Video abstract.

Insights into the Role of the Fungal Community in Variations of the Antibiotic Resistome in the Soil Collembolan Gut Microbiome

Fertilization is known to affect antibiotic-resistance gene (ARG) patterns in the soil, even in the gut of soil fauna. Here, we conducted a microcosm experiment to investigate differences of effects of different fertilizers on collembolan gut ARG profiles and to further explore the microecological mechanisms that cause the differences. Although fertilization increased the abundance of ARGs, compared with the conventional manure, the application of antibiotic-reduced manure and vermicompost all curbed the enrichment of ARGs in the gut of collembolans. The results of the structural equation model revealed that changes in the microbial community caused by fertilizations have an important contribution to variations in the ARGs. We further found that the fungal community, like bacterial community, is also an important driver of ARG patterns in the collembolan gut. The fungi belonging to Dokmaia and Talaromyces were significantly correlated with the ARGs in the gut of collembolans. In addition, the application of vermicompost significantly increased the abundance of agricultural beneficial microbes in the soil environment. Together, our results provide an insight into the role of the fungal community on ARG patterns in the soil collembolan gut microbiome and highlight environmental friendliness of vermicomposting.