Soil oxytetracycline exposure alters the microbial community and enhances the abundance of antibiotic resistance genes in the gut of Enchytraeus crypticus

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.

Global prediction of agricultural soil antibiotic susceptibility and safe boundary for biota

Pervasive anthropogenic activities release substantial quantities of antibiotics into soils, damaging soil organisms, introducing antibiotic resistance, and thus jeopardizing the safe boundaries for biodiversity. Here, by applying advanced geospatial modeling and establishing the planetary boundary (PB), we estimated that, at the baseline year (2015), global agricultural soil antibiotic concentration is 122.0 μg kg-1, within the PB of 153.7 μg kg-1 beyond which the health of soil biota (including bacteria, fungi, invertebrates, and antibiotic-resistance genes) decreases dramatically. In ∼2070, soil antibiotic concentrations increase while the boundaries decrease from SSP1-RCP2.6, SSP2-RCP4.5 to SSP5-RCP8.5. Under SSP5-RCP8.5, global soil organisms face the adverse antibiotic pollution (148.9 μg kg-1) that has transgressed the boundary (136.1 μg kg-1). Our study reveals the geopolitical inequality arising from antibiotic susceptibility and highlights the urgent need of the sustainable development to avoid catastrophic consequences on global soil organisms.

Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish

Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.

Antibiotics alter the metabolic profile of metolachlor in soil-plant system by disturbing the detoxifying process and oxidative stress

Antibiotics are widely detected in farmland, which may influence the environmental behavior and risks of the coexisting pesticide. In this work, the effects of antibiotics on metolachlor transformation in soil-pea and the risk of metolachlor to earthworm were assessed, and the mechanism was explored in view of detoxifying process and oxidative stress. Antibiotics affected not the degradation rate but the metabolic profile of metolachlor. In soil, the content of metabolites oxaloacetic acid (OA) and ethane sulfonic acid (ESA) was decreased and dechlorometolachlor (DCL) was increased by antibiotics. In pea, the accumulation of metolachlor, DCL and ESA was decreased, while OA was increased by antibiotics. The changed transformation of metolachlor affected the risk to earthworm according to risk quote assessment. In further research, it was found that cytochrome P450 (CYP450) enzyme was reduced by 12.3% - 30.4% in soil and 12.4% - 23.6% in pea, which might due to excessive ROS accumulation induced by antibiotics, thus affecting the transformation and metabolite profile of metolachlor in soil-plant system.

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.

Beneficial rhizosphere bacteria provides active assistance in resisting Aphis gossypiis in Ageratina adenophora

Ageratina adenophora can enhance its invasive ability by using beneficial rhizosphere bacteria. Bacillus cereus is able to promote plant growth and provide a positive feedback effect to A. adenophora. However, the interaction between A. adenophora and B. cereus under the influence of native polyphagous insect feeding is still unclear. In this study, Eupatorium lindleyanum, a local species closely related to A. adenophora, was used as a control, aimed to compare the content of B. cereus in the roots of A. adenophora and rhizosphere soil after different densities of Aphis gossypii feeding, and then investigated the variations in the population of A. gossypii and soil characteristics after the addition of B. cereus. The result showed that B. cereus content in the rhizosphere soil and root of A. adenophora increased significantly under A. gossypii feeding compared with local plants, which also led to the change of α-diversity and β-diversity of the bacterial community, as well as the increase in nitrate nitrogen (NO3 -N) content. The addition of B.cereus in the soil could also inhibit the population growth of A. gossypii on A. adenophora and increase the content of ammonium nitrogen (NH4 +-N) in the soil. Our research demonstrated that B. cereus enhances the ability of A. adenophora to resist natural enemy by increasing soil ammonium nitrogen (NH4 +-N) and accumulating other beneficial bacteria, which means that rhizosphere microorganisms help invasive plants defend themselves against local natural enemies by regulating the soil environment.

Biofilm enhances the interactive effects of microplastics and oxytetracycline on zebrafish intestine

The enhanced adsorption of pollutants on biofilm-developed microplastics has been proved in many studies, but the ecotoxicological effects of biofilm-developed microplastics on organisms are still unclear. In this study, adult zebrafish were exposed to original microplastics, biofilm-developed microplastics, original microplastics absorbed with oxytetracycline (OTC), and biofilm-developed microplastics absorbed with OTC for 30 days. The intestinal histological damage, intestinal biomarker response, gut microbiome and antibiotic resistance genes (ARGs) profile of zebrafish were measured to explore the roles of biofilm in the effects of microplastics. The results showed that biofilm-developed microplastics significantly increased the number of goblet cells in intestinal epithelium compared with the control group. The biofilm-developed microplastics also induced the oxidative response in the zebrafish intestines, and biofilm changed the response mode in the combined treatment with OTC. Additionally, the biofilm-developed microplastics caused intestinal microbiome dysbiosis, and induced the abundance of some pathogenic genera increasing by several times compared with the control group and the original microplastics treatments, regardless of OTC adsorption. Furthermore, the abundance of ARGs in biofilm-developed microplastics increased significantly compared with the control and the original microplastic treatments. This study emphasized the significant influence and unique role of biofilm in microplastic studies.

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.

Antibiotic resistance genes and the association with bacterial community in biofilms occurring during the drinking water granular activated carbon (GAC) sandwich biofiltration

The granular activated carbon (GAC) sandwich modification to slow sand filtration could be considered as a promising technology for improved drinking water quality. Biofilms developed on sand and GAC surfaces are expected to show a functional diversity during the biofiltration. Bench-scale GAC sandwich biofilters were set-up and run continuously with and without antibiotic exposure. Surface sand (the schmutzdecke) and GAC biofilms were sampled and subject to high-throughput qPCR for antibiotic resistance gene (ARG) analysis and 16 S rRNA amplicon sequencing. Similar diversity of ARG profile was found in both types of biofilms, suggesting that all ARG categories decreased in richness along the filter bed. In general, surface sand biofilm remained the most active layer with regards to the richness and abundance of ARGs, where GAC biofilms showed slightly lower ARG risks. Network analysis suggested that 10 taxonomic genera were implicated as possible ARG hosts, among which Nitrospira, Methyloversatilis and Methylotenera showed the highest correlation. Overall, this study was the first attempt to consider the whole structure of the GAC sandwich biofilter and results from this study could help to further understand the persistence of ARGs and their association with the microbial community in drinking water biofiltration system.

Ciprofloxacin enhances cadmium toxicity to earthworm Eisenia fetida by altering the gut microorganism composition

The concurrent existence of cadmium (Cd) and ciprofloxacin (CIP) in agricultural soils is very common, but presents a challenge to soil organisms. As more attention has been paid to the effect of toxic metals on the migration of antibiotic resistance genes, the critical role of the gut microbiota in CIP-modifying Cd toxicity in earthworms remains unclear. In this study, Eisenia fetida was exposed to Cd and CIP alone or in combination at environmentally relevant concentrations. Cd and CIP accumulation in earthworm increased as their respective spiked concentrations increased. In fact, Cd accumulation increased by 39.7% when 1 mg/kg CIP was added; however, the addition of Cd did not affect CIP uptake. Compared with exposure to Cd alone, a greater ingestion of Cd following combined exposure to Cd and 1 mg/kg CIP resulted in greater oxidative stress and energy metabolism disturbances in earthworms. The reactive oxygen species (ROS) contents and apoptosis rate of coelomocytes were more sensitive to Cd than these biochemical indicators. In fact, 1 mg/kg Cd induced the derivation of ROS. Similarly, the toxicity of Cd (5 mg/kg) to coelomocytes was promoted by CIP (1 mg/kg), ROS content in coelomocytes and the apoptosis rate increased by 29.2% and 113.1%, respectively, due to increased Cd accumulation. Further investigation of the gut microorganisms revealed that the decreased abundance of Streptomyces strains (known as Cd accumulation taxa) could be a critical factor for enhanced Cd accumulation and greater Cd toxicity to earthworms following exposure to both Cd and CIP; this was because this microorganism group was eliminated by the simultaneous ingestion of CIP. This study stressed the role of gut microorganisms in altering the toxicity of Cd and CIP combined contamination in soil organisms. More attention should be paid to the ecological risks of such combined contamination in soils.

Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome

Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.

The binding effect and photooxidation on oxytetracycline with algal extracellular polymeric substances and natural organic matter

Surface water contains a large amount of dissolved organic matter (DOM). Interactions between DOM and micropollutants have a significant impact on micropollutant degradation. In this study, algal extracellular polymeric substances (EPS) and natural organic matter (NOM) were selected as two DOM sources and oxytetracycline (OTC) as a representative micropollutant. EPS was mainly composed of tryptophan and protein-like organics, while NOM was mainly composed of fulvic acid-like, humic acid-like, and hydrophobic acid components. In addition, OTC degradation significantly decreased when bound with EPS and the C=O and C-H bonds of CH₂ or CH₃ groups may be involved in binding EPS and OTC, respectively, while -COOH may be involved in the binding of NOM and OTC. Furthermore, triplet intermediates were found to play a major role in OTC photodegradation in both EPS and NOM, with the contribution calculated as 49.96% and 44.61%, respectively. Steady-state concentrations of ³EPS* in EPS and ³NOM* in NOM were 3.59 × 10^-14 mol L^-1 and 5.54 × 10^-15 mol L^-1, respectively. These results provide new insights into the degradation of antibiotic-containing wastewater in the natural environment or engineering applications.

Combined effects of micro-/nano-plastics and oxytetracycline on the intestinal histopathology and microbiome in zebrafish (Danio rerio)

Accumulated evidence has demonstrated that microplastics and oxytetracycline (OTC) affect organisms, but few studies have investigated their combined effects on aquatic organisms. In this study, adult zebrafish (Danio rerio) were exposed to single and binary-combined contamination of micro-, nano-sized polystyrene plastics and OTC for 30 days, and the intestinal histopathology, gut microbiota and antibiotic resistance genes (ARGs) of zebrafish were measured. The results showed that the intestinal epithelial damage increase with the decrease of plastic sizes. Nano-sized plastics, OTC and their combined exposure caused intestinal epithelial damage, and co-exposure with micro-sized plastics reduced the intestinal damage caused by single OTC exposure. The gut microbial communities were affected by the combined exposure to microplastics and OTC. Compared with the blank control, the relative abundance of Fusobacteria increased 12.7 % and 21.1 % in OTC combined with 45-85 μm micro-plastics (MOTC) and 40-54 nm nano-plastics (NOTC), respectively, and that of Bacteroidetes increased 26.2 % and 18.6 % in the MOTC and NOTC treatments, respectively. The effects of MOTC and NOTC on the biodiversity of the zebrafish gut microbiome were different; MOTC increased the biodiversity by 11.3 % compared with the blank control, whereas NOTC decreased the biodiversity by 8.8 % compared with the blank control. Furthermore, the abundance of ARGs in 40-54 nm nano-plastics, MOTC and NOTC treatments was increased 96.9 %, 96.6 % and 68.8 % compared with the control group, respectively. Additionally, significant differences were observed in ARGs characteristics between the micro- and nano-plastics treated groups whether combined with OTC or not. These results are essential to further understand the combined ecotoxicological effects of micro- or nano-plastics and antibiotics on aquatic organisms.

Longitudinal analysis of exposure to a low concentration of oxytetracycline on the zebrafish gut microbiome

Oxytetracycline, a widely produced and administered antibiotic, is uncontrollably released in low concentrations in various types of environments. However, the impact of exposure to such low concentrations of antibiotics on the host remains poorly understood. In this study, we exposed zebrafish to a low concentration (5,000 ng/L) of oxytetracycline for 1 month, collected samples longitudinally (Baseline, and Days 3, 6, 9, 12, 24, and 30), and elucidated the impact of exposure on microbial composition, antibiotic resistance genes, mobile genetic elements, and phospholipid metabolism pathway through comparison of the sequenced data with respective sequence databases. We identified Pseudomonas aeruginosa, a well-known pathogen, to be significantly positively associated with the duration of oxytetracycline exposure (Adjusted P = 5.829e-03). Several tetracycline resistance genes (e.g., tetE) not only showed significantly higher abundance in the exposed samples but were also positively associated with the duration of exposure (Adjusted P = 1.114e-02). Furthermore, in the exposed group, the relative abundance of genes involved in phospholipid metabolism had also decreased. Lastly, we characterized the impact of exposure on zebrafish intestinal structure and found that the goblet cell counts were decreased (~82%) after exposure. Overall, our results show that a low concentration of oxytetracycline can increase the abundance of pathogenic bacteria and lower the abundance of key metabolic pathways in the zebrafish gut microbiome that can render them prone to bacterial infections and health-associated complications.

Automated detection and quantification of Enchytraeus crypticus (Oligochaeta: Enchytraeidae) in tropical artificial soil using image analysis

The effects of toxic substance in soil matrices are evaluated by assessing adult worm survival and reproduction. Throughout the test, hundreds of juvenile potworms can be found. The current method for Enchytraeus crypticus quantification in soil samples is a laborious and time-consuming procedure that involves manual counting. The present work proposes a method for quick and reliable counting of E. crypticus by using an automated image analysis algorithm applied to soil images. Comparisons between automated and manual methods conducted in double-blind trials involving a large, routine batch of tropical artificial soil samples revealed no statistically significant differences for a wide range of worm densities. The proposed method overcomes time-consuming counts in manual methods and is suited to be deployed routinely for soil toxicity studies involving large batches of samples.

Toxicity assessment and microbial response to soil antibiotic exposure: differences between individual and mixed antibiotics

Increasing amounts of antibiotics are introduced into soils, raising great concerns on their ecotoxicological impacts on the soil environment. This work investigated the individual and joint toxicity of three antibiotics, tetracycline (TC), sulfonamide (SD) and erythromycin (EM) via a whole-cell bioreporter assay. TC, SD and EM in aqueous solution demonstrated cytotoxicity, whilst soil exposure showed genotoxicity, indicating that soil particles possibly affected the bioavailability of antibiotics. Toxicity of soils exposed to TC, SD and EM changed over time, demonstrating cytotoxic effects within 14-d exposure and genotoxic effects after 30 days. Joint toxicity of TC, SD and EM in soils instead showed cytotoxicity, suggesting a synergetic effect. High-throughput sequencing suggested that the soil microbial response to individual antibiotics and their mixtures showed a different pattern. Soil microbial community composition was more sensitive to TC, in which the abundance of Pseudomonas, Pirellula, Subdivision3_genera_incertae_sedis and Gemmata varied significantly. Microbial community functions were significantly shifted by EM amendments, including signal transduction mechanisms, cytoskeleton, cell wall/membrane/envelope biogenesis, transcription, chromatin structure and dynamics, and carbohydrate transport and metabolism. This work contributes to a better understanding of the ecological effects and potential risks of individual and joint antibiotics on the soil environment.

Fluoroquinolone antibiotics disturb the defense system, gut microbiome, and antibiotic resistance genes of Enchytraeus crypticus

Antibiotic residues from animal manure cause soil pollution and can pose a threat to soil animals. In this study, the toxicological effects of fluoroquinolone antibiotics on Enchytraeus crypticus, including defence response, gut microbiome, and antibiotic resistance genes (ARGs), were studied. The cytochrome P450 enzyme activity and reactive oxygen species levels increased, activating the defense response. The superoxide dismutase and glutathione S-transferase activity, and the expression of immune defense molecules such as coelomic cytolytic factor, lysozyme, bactericidal protein fetidins and lysenin changed. Furthermore, the diversity of the gut microbiome decreased, and the relative abundance of Bacteroidetes decreased significantly at the phylum level but increased in pathogenic and antibiotic-secreting bacteria (Rhodococcus and Streptomyces) at the genus level. However, the soil microbiome was not significantly different from that of the control group. The relative abundance of ARGs in the gut and soil microbiome significantly increased with enrofloxacin concentration, and the fluoroquinolone ARGs were significantly increased in both the soil (20.85-fold, p < 0.001) and gut (11.72-fold, p < 0.001) microbiomes. Subtypes of ARGs showed a positive correlation with Rhodococcus, which might increase the risk of disease transmission and the probability of drug-resistant pathogens. Furthermore, mobile genetic elements significantly promote the spread of ARGs.

Evaluating the interaction of soil microorganisms and gut of soil fauna on the fate and spread of antibiotic resistance genes in digested sludge-amended soil ecosystem

Earthworms have shown their effectiveness in reducing the abundances of antibiotic resistance genes (ARGs) from solid waste. However, the mechanisms of the reduced ARGs by earthworm and whether the solid waste would affect the ARGs profile in earthworm gut were poorly understood. Herein, the patterns of ARGs and microbial communities in digested sludge-amended soil and earthworm gut after 80-day cultivation were investigated. Results show that the enrichment of ARGs (e.g., tetA, tetQ, and sulII) in soil caused by digested sludge-amendment was temporary and would recover to their original levels before amendment. In addition, earthworms could contribute to the further reduction of ARG abundances, which was mainly attributed to their gut digestion via shifting the microbial community (e.g., attenuating the anaerobes). However, the amended soil could significantly increase ARGs abundance in the earthworm gut, which may enhance the potential risk of ARGs spread via the food chain. These findings may provide a new sight on the control of ARGs occurrence and dissemination in sludge-amended soil ecosystem with consideration of earthworms.

Macleaya cordata extract, an antibiotic alternative, does not contribute to antibiotic resistance gene dissemination

The abuse of antibiotics and their associated health risks are receiving global attention. The use of antibiotic additives in fodder has been banned in the European Union since 2006 and in China since 2020. Antibiotic alternatives are being developed, but their risks to the soil ecosystem remain poorly understood. Here, we compared the effects of the antibiotic oxytetracycline (OTC10, 10 mg/kg) with those of a Macleaya cordata extract (MCE, 10 and 100 mg/kg), the major antibiotic substitute. All tested concentrations of MCE and OTC10 exerted slight effects on the soil microbiome, but OTC10 and MCE100 could interfere with the structures and functions of the gut microbiome and might thus affect the soil ecological functions of Enchytraeus crypticus. Furthermore, OTC10 exposure inevitably increased the antibiotic resistance gene (ARG) abundance by 213%, whereas MCE did not induce ARG dissemination, which explains why MCE is considered to be associated with a low ecological risk. Our research provides the first demonstration of the risks posed by antibiotic alternatives to soil animals from the perspective of environmental toxicology and explores the potential development of antibiotic alternatives associated with a low ecological risk from a new perspective.

Environmental concentrations of antibiotics alter the zebrafish gut microbiome structure and potential functions

A paradoxical impact of high rates of production and consumption of antibiotics is their widespread release in the environment. Consequently, low concentrations of antibiotics and their byproducts have been routinely identified from various environmental settings especially from aquatic environments. However, the impact of such low concentrations of antibiotics on the exposed host especially in early life remains poorly understood. We exposed zebrafish to two different environmental concentrations of oxytetracycline and sulfamethoxazole, from larval stage to adulthood (∼120 days) and characterized their impact on the taxonomic diversity, antibiotic resistance genes, and metabolic pathways of the gut microbiome using metagenomic shotgun sequencing and analysis. Long term exposure of environmental concentrations of oxytetracycline and sulfamethoxazole significantly impacted the taxonomic composition and metabolic pathways of zebrafish gut microbiome. The antibiotic exposed samples exhibited significant enrichment of multiple flavobacterial species, including Flavobacterium sp. F52, Flavobacterium johnsoniae and Flavobacterium sp. Fl, which are well known pathogenic bacteria. The relative abundance of antibiotic resistance genes, especially several tetratcycline and sulfonamide resistance genes were significantly higher in the exposed samples and showed a linear correlation with the antibiotic concentrations. Furthermore, several metabolic pathways, including folate biosynthesis, oxidative phosphorylation, and biotin metabolism pathways, showed significant enrichment in the antibiotic exposed samples. Collectively, our results suggest that early life exposure of the environmental concentrations of antibiotics can increase the abundance of unfavorable bacteria, antibiotic resistance genes and associated pathways in the gut microbiome of zebrafish.

The equine hindgut as a reservoir of mobile genetic elements and antimicrobial resistance genes

Antibiotic resistance in bacterial pathogens is a growing problem for both human and veterinary medicine. Mobile genetic elements (MGEs) such as plasmids, transposons, and integrons enable the spread of antibiotic resistance genes (ARGs) among bacteria, and the overuse of antibiotics drives this process by providing the selection pressure for resistance genes to establish and persist in bacterial populations. Because bacteria, MGEs, and resistance genes can readily spread between different ecological compartments (e.g. soil, plants, animals, humans, wastewater), a "One Health" approach is needed to combat this problem. The equine hindgut is an understudied but potentially significant reservoir of ARGs and MGEs, since horses have close contact with humans, their manure is used in agriculture, they have a dense microbiome of both bacteria and fungi, and many antimicrobials used for equine treatment are also used in human medicine. Here, we collate information to date about resistance genes, plasmids, and class 1 integrons from equine-derived bacteria, we discuss why the equine hindgut deserves increased attention as a potential reservoir of ARGs, and we suggest ways to minimize the selection for ARGs in horses, in order to prevent their spread to the wider community.

Novel class 1 integron harboring antibiotic resistance genes in wastewater-derived bacteria as revealed by functional metagenomics

Combatting antibiotic resistance is critical to our ability to treat infectious diseases. Here, we identified and characterized diverse antimicrobial resistance genes, including potentially mobile elements, from synthetic wastewater treatment microcosms exposed to the antibacterial agent triclosan. After seven weeks of exposure, the microcosms were subjected to functional metagenomic selection across 13 antimicrobials. This was achieved by cloning the combined genetic material from the microcosms, introducing this genetic library into E. coli, and selecting for clones that grew on media supplemented with one of the 13 antimicrobials. We recovered resistant clones capable of growth on media supplemented with a single antimicrobial, yielding 13 clones conferring resistance to at least one antimicrobial agent. Antibiotic susceptibility analysis revealed resistance ranging from 4 to >50 fold more resistant, while one clone showed resistance to multiple antibiotics. Using both Sanger and SMRT sequencing, we identified the predicted active gene(s) on each clone. One clone that conferred resistance to tetracycline contained a gene encoding a novel tetA-type efflux pump that was named TetA(62). Three clones contained predicted active genes on class 1 integrons. One integron had a previously unreported genetic arrangement and was named In1875. This study demonstrated the diversity and potential for spread of resistance genes present in human-impacted environments.

Ecological role of earthworm intestinal bacteria in terrestrial environments: A review

Increasing evidence demonstrated the critical role the earthworm gut played in sustaining earthworm's metabolism and transformation of nutrients and pollutants in the environment. Being rich in nutrients, the earthworm gut is favorable for the colonization of (facultative) anaerobic bacteria, which bridge the host earthworm gut with adjacent terrestrial environment. Therefore, the status quo of earthworm gut research was primarily reviewed in this work. It was found that most studies focused on the bacterial composition and diversity of the earthworm gut, and their potential application in nutrient element and pollutant transformation, such as nitrification, methanogens, heavy metal detoxification, etc. Yet limited information was available about the specific mechanism of intestinal bacteria in nutrient and pollutant transformation. Therefore, in this work we highlighted the current problems and concluded the future prospect of worm's intestinal bacteria research. On one hand, high throughput sequencing and bioinformatics tools are critical to break the bottleneck in the intestinal bacteria research via clarifying the molecular mechanism involved in the transformation processes described above. In addition, a global dataset concerning worm gut bacteria will be needed to provide comprehensive information about intestinal bacteria pool, and act as a communication platform to further encourage the progress of worm gut research.

Microplastics combined with tetracycline in soils facilitate the formation of antibiotic resistance in the Enchytraeus crypticus microbiome

Growing evidence suggests that microplastics can adsorb antibiotics and may consequently exacerbate effects on the health of exposed organisms. Our current understanding of the combined effects of microplastics and antibiotics on antibiotic resistance genes (ARGs) in soil invertebrates is limited. This study aimed to investigate changes in the microbiome and ARGs in Enchytraeus crypticus following exposure to a soil environment that contained both microplastics and antibiotics. Tetracycline (TC), polyamide (PA) and polyvinyl chloride (PVC) were used to construct microcosms of polluted soil environments (TC, PA, PVC, PA+TC, PVC+TC). The differences in microbiomes and ARGs were determined by bacterial 16S rRNA gene amplicon sequencing and high throughput quantitative PCR. The results show that compared with the Control or microplastics alone treatments, TC was significantly accumulated in E. crypticus when exposed to TC alone or in combination with microplastics (P < 0.05), but there were no significant differences about TC accumulation between TC, PA+TC, and PVC+TC treated E. crypticus (P > 0.05). Microplastics and TC significantly disturbed the microbial community, and decreased the microbial alpha diversity of E. crypticus (P < 0.05). However, there were no significant differences between TC, microplastics and their combined exposure treatments, and no toxic synergies on the diversity of E. crypticus microbiome between tetracycline and microplastics in soil environment. All the treatments increased the diversity of ARGs in E. crypticus (39-49 ARGs vs. 25 ARGs of control). In particular, treatments combining PVC and TC or PA and TC exposure resulted in greater ARGs abundance than the treatments when E. crypticus was exposed to PVC, PA or TC alone. These results add to our understanding of the combined effects of microplastics and antibiotics on the ARGs and microbiome of soil invertebrates.

Antibiotic Resistance in the Collembolan Gut Microbiome Accelerated by the Nonantibiotic Drug Carbamazepine

The effects of pharmaceuticals as emerging contaminants in soil on the gut microbiome and antibiotic resistome in nontarget soil fauna are largely elusive. In this study, we explored the composition of the bacterial community and the presence of antibiotic resistance genes (ARGs) in the gut of the model soil collembolan (Folsomia candida) upon antiepileptic drug carbamazepine (CBZ) and antibiotic tetracycline (TC) exposure. Results showed that, individually or in combination, exposure to TC or CBZ significantly altered the gut community structure of F. candida, causing some enrichment of the bacteria associated with xenobiotic metabolism, such as Arthrobacter, Achromobacter, Gordonia, and Shinella. More importantly, oral exposure to the nonantibiotic drug CBZ enhanced the abundance and diversity of ARGs in the gut of F. candida, especially for the beta-lactams and multidrug resistance genes. Our results revealed that the most likely hosts of ARGs in the gut of F. candida were Proteobacteria and Actinobacteria. The significant positive correlation between mobile genetic elements (MGEs) and ARGs indicated the potential risk of ARGs transmission in the gut of F. candida. Overall, the nonantibiotic CBZ is likely to disturb the gut microbiota of nontarget soil fauna such as collembolans, thereby enhancing the dissemination of ARGs.

World within world: Intestinal bacteria combining physiological parameters to investigate the response of Metaphire guillelmi to tetracycline stress

Due to the abusive usage of antibiotics in animal husbandry, a large amount of residual antibiotics has been released into the environment, therein posing great threat against both environment security and public health. Therefore, it is of great significance to investigate the toxicity of antibiotics on the widely-applied bioindicator-earthworm. In this work, the physiological parameters and the intestinal bacteria community of Metaphire guillelmi were monitored simultaneously to evaluate their sensitivity to the tetracycline (TC) exposure. As expected, the antioxidant enzyme activity and coelomocyte apoptosis acted fairly well as biomarkers for the TC toxicity. In contrast, the intestinal bacteria of Metaphire guillelmi responded varyingly to different TC doses. When TC concentration increased from 0 to 35.7 μg cm^-2, the percentage of the Proteobacteria phylum declined significantly from 85.5% to 34.4%, while the proportions of the Firmicutes, Planctomycetes and Atinomycete phyla clearly increased (p < 0.05). Meanwhile, the levels of TC resistance genes tetA, tetC, and tetW increased with the increasing TC concentration, in contrast to the declined abundance in denitrifying genes nirS and nosZ (p < 0.05). By analyzing the correlation between the antioxidant enzyme activity and the dominant intestinal bacteria in the worm gut, it is interesting to found that the four dominant bacteria genera Mesorhizobium, Aliihoeflea, Romboutsia, and Nitrospira are the promising bioindicator of TC stress due to their sensitive response. This work shed novel light on evaluating the ecotoxicological risks posed by residual TC in environment by using a combination of physiological parameters and intestinal bacterial activity in earthworms.

An innovative modeling approach of linking land use patterns with soil antibiotic contamination in peri-urban areas

Due to the intensive use and continuous release, high and persistent concentrations of antibiotics are found in soils worldwide. This severe contamination elevates the risks associated with antibiotic exposure and resistance for soil ecosystems and human health. Estimating antibiotic concentrations in soils is a complex and important challenge because the limited information is available on antibiotic use and emission and the high exposure risk to human health occurred in peri-urban areas. In this study, soil antibiotic contamination was linked with land use patterns in a data-scarce peri-urban area in four different seasons, and we established a modeling framework based on land use to estimate spatially explicit distribution of antibiotics in soils. The soil antibiotic concentration was found to be substantially affected by surrounding land use patterns in buffer zones with a radius of 350 m. Agricultural land was the main source of antibiotics entering the soil. Notably, road networks also had considerable impacts on antibiotic residues in soils. Then, a statistical model was developed in describing the linkage between land use patterns and soil antibiotic concentration. Model evaluation suggested that the proposed model successfully simulated the variation of antibiotics in soil with good statistical performance (R² > 0.7). Finally, the model was extrapolated to investigate detailed distribution of antibiotics in soils. Clear spatial and seasonal dynamics can be found in soil antibiotic concentration. To our knowledge, this was the first attempt to adopt a model focusing on land use pattern to estimate the spatially explicit distribution of antibiotics in soils. Despite of some uncertainties, the research provides a land-use-based modeling approach as a reference for preventing and controlling soil antibiotic contamination in the future.

Does soil CuO nanoparticles pollution alter the gut microbiota and resistome of Enchytraeus crypticus?

Growing evidence suggests that metallic oxide nanoparticles can pose a severe risk to the health of invertebrates. Previous attention has been mostly paid to the effects of metallic oxide nanoparticles on the survival, growth and physiology of animals. In comparison, the effects on gut microbiota and incidence of antibiotic resistance genes (ARGs) in soil fauna remain poorly understood. We conducted a microcosm study to explore the responses of the non-target soil invertebrate Enchytraeus crypticus gut microbiota and resistomes to copper oxide nanoparticles (CuO NPs) and copper nitrate by using bacterial 16S rRNA gene amplicons sequencing and high throughput quantitative PCR. The results showed that exposure to Cu²⁺ resulted in higher bioaccumulation (P < 0.05) and lower body weight and reproduction (P < 0.05) of Enchytraeus crypticus than exposure to CuO NPs. Nevertheless, exposure to CuO NPs for 21 days markedly increased the alpha-diversity of the gut microbiota of Enchytraeus crypticus (P < 0.05) and shifted the gut microbial communities, with a significant decline in the relative abundance of the phylum Planctomycetes (from 37.26% to 19.80%, P < 0.05) and a significant elevation in the relative abundance of the phyla Bacteroidetes, Firmicutes and Acidobacteria (P < 0.05). The number of detected ARGs in the Enchytraeus crypticus gut significantly decreased from 45 in the Control treatment to 16 in the Cu(NO₃)₂ treatment and 20 in the CuO NPs treatment. The abundance of ARGs in the Enchytraeus crypticus gut were also significantly decreased to 38.48% when exposure to Cu(NO₃)₂ and 44.90% when exposure to CuO NPs (P < 0.05) compared with the controls. These results extend our understanding of the effects of metallic oxide nanoparticles on the gut microbiota and resistome of soil invertebrates.

Bioremediation of tetracycline antibiotics-contaminated soil by bioaugmentation

Bioaugmentation using specific microbial strains or consortia was deemed to be a useful bioremediation technology for increasing bioremediation efficiency. The present study confirmed the effectiveness and feasibility of bioaugmentation capability of the bacterium BC immobilized on sugarcane bagasse (SCB) for degradation of tetracycline antibiotics (TCAs) in soil. It was found that an inoculation dose of 15% (v/w), 28–43 °C, slightly acidic pH (4.5–6.5), and the addition of oxytetracycline (OTC, from 80 mg kg⁻¹ to 160 mg kg⁻¹) favored the bioaugmentation capability of the bacterium BC, indicating its strong tolerance to high temperature, pH, and high substrate concentrations. Moreover, SCB-immobilized bacterium BC system exhibited strong tolerance to heavy metal ions, such as Pb²⁺ and Cd²⁺, and could fit into the simulated soil environment very well. In addition, the bioaugmentation and metabolism of the co-culture with various microbes was a complicated process, and was closely related to various species of bacteria. Finally, in the dual-substrate co-biodegradation system, the presence of TC at low concentrations contributed to substantial biomass growth but simultaneously led to a decline in OTC biodegradation efficiency by the SCB-immobilized bacterium BC. As the total antibiotic concentration was increased, the OTC degradation efficiency decreased gradually, while the TC degradation efficiency still exhibited a slow rise tendency. Moreover, the TC was preferentially consumed and degraded by continuous introduction of OTC into the system during the bioremediation treatment. Therefore, we propose that the SCB-immobilized bacterium BC exhibits great potential in the bioremediation of TCAs-contaminated environments.

Bioaugmentation using specific microbial strains or consortia was deemed to be a useful bioremediation technology for increasing bioremediation efficiency.