Polycyclic aromatic hydrocarbons (PAHs) enriching antibiotic resistance genes (ARGs) in the soils

Rising Tide to Silent Tsunami: Unveiling the role of plastics in driving antimicrobial resistance

Pollution caused by plastic production and waste has severe consequences on global economies, social inequalities, and ecosystems. Likewise, antimicrobial resistance (AMR) is one of the greatest One Health challenges. These threats are typically considered in isolation, but there is likely a complex interplay between the two. By adopting a systems approach and looking across the whole life cycle of plastics, we propose the range of ways in which plastic may influence AMR. Starting with raw material extraction processes where the leaching of potentially AMR co-selective chemicals used in pumping or piping of plastic feedstocks may influence AMR development in environmental microbial communities. Then, during production and manufacture, the use of plastic additives may impose selection for AMR. Finally, during use, collection or disposal, plastics can transport AMR biofilms in the community, clinical, agricultural, or aquatic settings. By linking these two important One Health threats, we may be better equipped and informed to combat them.

A microbial-driven persulfate activating-cycling system for in-depth oxytetracycline degradation and bacterial antibiotic resistance control

Insufficient biodegradability of antibiotics (e.g., oxytetracycline, OTC) and the accompanying antibiotic resistance gene (ARG) spreading risk have been a serious concern in wastewater treatment plants. This study developed a microbial-driven persulfate activating-cycling system (MPCS) relying on the iron-reducing capacity of Shewanella oneidensis to sustainably degrade OTC and prevent ARG elevation. In MPCS, a nanosized bio-magnet shell (20-60 nm) was bio-generated and incorporated with S. oneidensis to activate peroxydisulfate and produce free radicals to attack OTC, removed by 98.78 % in 120 min. S. oneidensis metabolism re-generated the bio-magnet and cleared the toxic intermediates. Despite the stress of OTC and free radicals, S. oneidensis sustained (live/death ratio of 74.50 %: 25.50 %) under bio-magnet shell protection, showing a strong energy metabolism and iron-reducing strength. The tight coupling of biodegradation and advanced oxidation process (AOP) greatly improved degrading efficiency (132.65 %-2369.44 % higher than single biodegradation or AOP). MPCS continuously operated 5 cycles efficiently, exhibiting a diverse degrading pathway with less toxic intermediates than the single treatment. Notably, MPCS functioned well without peroxydisulfate, as the S. oneidensis produces low-level hydrogen peroxide as the AOP substrate, achieving favorable OTC elimination. Especially, the expression of sixteen tetracycline-related ARGs dropped by 62.94 %-100 % in MPCS than biodegradation, indicating resistance control advantage under bio-magnet shell protection and the synergism effect of AOP and biodegradation. This study spontaneously recyclably combined biodegradation and AOP to simultaneously eliminate antibiotics and ARGs, which provided a potential approach to control the drug resistance risk.

The fate and ecological risk of mefentrifluconazole in the water-sediment system: A systematic analysis at the enantiomer level

Triazole fungicides occupy a significant position in the global fungicidal market. Mefentrifluconazole (MFZ) is a new-generation chiral triazole fungicide with broad applications. It can effectively control several rice fungal diseases; thus, its wide application increases its risk of entering the water and sediment in ecosystems. In this study, the stereoselective fate and risk of MFZ in the water-sediment system were investigated. The results showed stereoselective differences in the acute toxicity and fate of MFZ enantiomers (S-MFZ and R-MFZ) in the water-sediment system, with S-MFZ being more toxic and persistent. Both R-MFZ and S-MFZ induced significant decreases in the oxidation-reduction potential (ORP) value and organic matter (OM) content of the sediment. Additionally, soil enzyme activity in the sediments changed in varying degrees during exposure. Further microbiome sequencing results showed that both R-MFZ and S-MFZ induced changes in the composition of sediment microbial communities and decreased species diversity, which, in turn, affected the metabolic processes of microorganisms and the function of glycosyltransferase (GT) enzymes, especially S-MFZ. Correlation analysis showed that stereoselectivity in the interaction between the MFZ enantiomers and GT enzymes induced a difference in the synthesis of lipopolysaccharides; thus, affecting the abundances of the relevant bacterial genera and carbohydrate metabolic pathways. Exposure to MFZ enantiomers induced an increase in the abundance of anaerobic bacteria, such as Methylophilus and Rhodoferax, which exacerbated the anaerobic environment of the sediment system, leading to acidification and accelerated nutrient decomposition.

Enhanced heterotrophic denitrification in groundwater using pretreated Ginkgo biloba leaves: Optimized carbon utilization and metabolic function diversity

Ginkgo biloba leaves (Gbl), as abundant agricultural and forestry residues which contains the quercetin that plays an important role in mediating electron transfer, represent a promising heterotrophic denitrification carbon source. Nonetheless, challenges persist due to concerns over nitrate leaching. This study pioneers the application of pretreated Gbl as external carbon sources for heterotrophic denitrification, with a focus on enhancing carbon bioavailability and mitigating nitrate leaching risks. Among the pretreatment strategies employed, the extraction process effectively eliminated NO3--N leaching, while the fermentation process reduced it by 52.8%. The saturated total organic carbon (TOC) concentration per unit mass of fermented Gbl was marginally lower compared to untreated leaves, yet the secondary kinetic reaction constant increased from 10.94 to 12.91 mg/(g·h·L), indicating an accelerated organic carbon release rate. Fermentation with Eurotium cristatum disrupted the rigid lignocellulose structure, thereby enhancing carbon source bioavailability. This resulted in a significant increase in alcohols in the leaching solution, from 27.0% to 68.6%, and a substantial reduction in aromatic compounds, from 20.2% to 0.2%, which alleviated microbial toxicity. In terms of denitrification performance, fermented Ginkgo biloba leaves (Fl) outperformed Ginkgo biloba extract residue leaves (Erl), which in turn surpassed untreated Gbl. Both Fl and Erl demonstrated robust adaptability across a broad pH range of 5.0-11.0. Under neutral conditions, the Fl system exhibited the highest primary kinetic constant for nitrate removal, reaching 0.0494 h⁻1. Microbial community revealed that all three carbon sources harbored denitrification and lignocellulose degradation capabilities. Notably, the Fl and Erl systems exhibited enhanced carbohydrate transport (G), amino acid transport (E), and inorganic ion transport (P), underscoring the potential pretreatments to optimize carbon source utilization. Collectively, these findings affirm the viability of Gbl as a carbon source for heterotrophic denitrification, providing valuable insights for its application in addressing nitrate pollution in aquatic environments.

Understanding pollutant-driven shifts of antibiotic resistome in activated sludge: A lab-scale study

Non-antibiotic pollutants have been identified as contributors to the development of antibiotic resistance across various environments. Wastewater treatment plants, recognized as hotspots for antibiotic resistance genes (ARGs), have received extensive attention regarding the mechanisms driving resistance changes in activated sludge. However, the specific impacts of heavy metals and aromatic organics-common pollutants in industrial wastewater-on the resistome of activated sludge, as well as the underlying mechanisms driving these effects, remain underexplored. In this study, we investigated the bacterial community and ARGs in activated sludge under the stress of three heavy metals and three aromatic organics. Our results revealed that both heavy metals and organics led to an increase in the total abundance of ARGs. Notably, the bacA and sul1 genes exhibited the highest abundance under both stress conditions, serving as indicative ARGs of the activated sludge resistome. The elevated ARG abundance was directly linked to shifts in the bacterial community induced by stress from heavy metals and aromatic organics, indicating an indirect co-selection of ARGs via metal resistance genes and aromatic degrading genes. Despite the overall increase in ARG abundance, the proportion of high-risk ARGs did not rise, suggesting that higher ARG abundance does not necessarily correlate with an elevated risk.

Effects of decabromodiphenyl ethane (DBDPE) exposure on soil microbial community: Nitrogen cycle, microbial defense and repair and antibiotic resistance genes transfer

DBDPE, a widely used brominated flame retardant, is frequently detected in soil. However, the toxic effects of DBDPE on soil microbial communities remain unclear. This study investigated the effects of DBDPE on the microbial community shifts, the nitrogen cycle, microbial defense and repair, and antibiotic resistance genes (ARGs) transfer. After 28 days of DBDPE exposure, the soil microbial community was altered. Denitrifier were enriched by 4.07-78.22% under DBDPE exposure concentrations of 100-1000 ng/g. Additionally, the abundances of genes encoding enzymes involved in nitrification and denitrification processes were up-regulated at 100 ng/g DBDPE exposure, and further promoted at 1000 ng/g DBDPE exposure. Meanwhile, DBDPE exposure at concentrations of 100-1000 ng/g stimulated the production of extracellular polymers substances (EPS) (2155-2347 mg/kg), increased the accumulation of reactive oxygen species (ROS) (by 97.95-108.38%), and activated the antioxidant defense system of soil microorganisms, which correspondingly down-regulated catalase (CAT) genes (by 4.65-4.91%), while up-regulated superoxide dismutase (SOD) (by 0.52-2.63%) and glutathione (GSH) genes (by 19.03%-44.61%). Genes related to the tricarboxylic acid (TCA) cycle, glycerophospholipid metabolism, and peptidoglycan biosynthesis were up-regulated, enhancing cell membrane repair in response to DBDPE exposure. Moreover, the increase in DBDPE concentration selectively enriched and promoted the transmission of ARGs. The co-occurrence network of ARGs and mobile genetic elements (MGEs) revealed that DBDPE facilitated the horizontal gene transfer (HGT)-mediated transmission of transposase, ist, and insertion sequence-associated ARGs.

Genome-resolved analysis of Serratia marcescens strain SMTT infers niche specialization as a hydrocarbon-degrader

Bacteria that are chronically exposed to high levels of pollutants demonstrate genomic and corresponding metabolic diversity that complement their strategies for adaptation to hydrocarbon-rich environments. Whole genome sequencing was carried out to infer functional traits of Serratia marcescens strain SMTT recovered from soil contaminated with crude oil. The genome size (Mb) was 5,013,981 with a total gene count of 4,842. Comparative analyses with carefully selected S. marcescens strains, 2 of which are associated with contaminated soil, show conservation of central metabolic pathways in addition to intra-specific genetic diversity and metabolic flexibility. Genome comparisons also indicated an enrichment of genes associated with multidrug resistance and efflux pumps for SMTT. The SMTT genome contained genes that enable the catabolism of aromatic compounds via the protocatechuate para-degradation pathway, in addition to meta-cleavage of catechol (meta-cleavage pathway II); gene enrichment for aromatic compound degradation was markedly higher for SMTT compared to the other S. marcescens strains analysed. Our data presents a valuable genetic inventory for future studies on strains of S. marcescens and provides insights into those genomic features of SMTT with industrial potential.

Metagenomic approaches in bioremediation of environmental pollutants

Metagenomics has emerged as a pivotal tool in bioremediation, providing a deeper understanding of the structure and function of the microbial communities involved in pollutant degradation. By circumventing the limitations of traditional culture-based methods, metagenomics enables comprehensive analysis of microbial ecosystems and facilitates the identification of new genes and metabolic pathways that are critical for bioremediation. Advanced sequencing technologies combined with computational and bioinformatics approaches have greatly enhanced our ability to detect sources of pollution and monitor dynamic changes in microbial communities during the bioremediation process. These tools enable the precise identification of key microbial players and their functional roles, and provide a deeper understanding of complex biodegradation networks. The integration of artificial intelligence (AI) with machine learning algorithms has accelerated the process of discovery of novel genes associated with bioremediation and has optimized metabolic pathway prediction. Novel strategies, including sequencing techniques and AI-assisted analysis, have the potential to revolutionize bioremediation by enabling the development of highly efficient, targeted, and sustainable remediation strategies for various contaminated environments. However, the complexity of microbial interactions, data interpretation, and high cost of these advanced technologies remain challenging. Future research should focus on improving computational tools, reducing costs, and integrating multidisciplinary approaches to overcome these limitations.

Fluoranthene slow down sulfamethazine migration in soil via π-π interaction to increase the abundance of antibiotic resistance genes

Sulfonamide antibiotics and polycyclic aromatic hydrocarbons (PAHs) often coexist in soil, leading to compound pollution through various pathways. This study focuses on sulfamethazine (SMZ) and PAHs (fluoranthene) as the subject for compound pollution research. Using a soil-groundwater simulation system, we investigated the migration characteristics of SMZ under coexistence with fluoranthene (Fla) and observed variations in the abundance of antibiotic resistance genes (ARGs). Through molecular docking simulations and isothermal adsorption experiments, we discovered that Fla bound with SMZ via π-π interactions, resulting in a 20.9% increase in the SMZ soil-water partition coefficient. Under compound conditions, the concentration of SMZ in surface soil could reach 1.4 times that of SMZ added alone, with an 13.4% extension in SMZ half-life. The deceleration of SMZ's vertical migration rate placed additional stress on surface soil microbiota, leading to a proliferation of ARGs by 66.3%-125.8%. Moreover, under compound pollution, certain potential hosts like Comamonadaceae and Gemmatimonas exhibited a significant positive correlation with resistance genes such as sul 1 and sul 2. These findings shed light on the impact of PAHs on sulfonamide antibiotic migration and the abundance of ARGs. They also provide theoretical insights for the development of technologies aimed at mitigating compound pollution in soil.

Masks As a New Hotspot for Antibiotic Resistance Gene Spread: Reveal the Contribution of Atmospheric Pollutants and Potential Risks

The consumption of disposable surgical masks (DSMs) considerably increased during the coronavirus pandemic in 2019. Herein, we explored the spread of antibiotic resistance genes (ARGs) and the potential risks of antibiotic resistant bacteria (ARB) on DSMs. At environmentally relevant concentrations, the conjugate transfer frequency (CTF) of ARGs increased by 1.34-2.37 folds by 20 μg/m3 of atmospheric water-soluble inorganic ions (WSIIs), and it increased by 2.62-2.86 folds by 80 ng/m3 of polycyclic aromatic hydrocarbons (PAHs). Total suspended particulates (TSP) further promoted the CTF in combination with WSIIs or PAHs. Under WSII and PAH exposure, gene expression levels related to oxidative stress, cell membrane, and the adenosine triphosphate (ATP) were upregulated. WSIIs predominantly induced cellular contact, while PAHs triggered ATP formation and membrane damage. Molecular dynamics simulations showed that WSIIs and PAHs reduced membrane lipid fluidity and increased membrane permeability through interactions with the phosphatidylcholine bilayer. DSM filtering performance decreased, and the CTF of ARGs increased with the wearing time. The gut simulator test showed that ARB disrupted the human gut microbial community and increased total ARG abundance but did not change the ARG abundance carried by ARB themselves. A mathematical model showed that long-term WSII and PAH exposure accelerated ARG dissemination in DSMs.

Effectiveness of low-intensity ultrasound on anaerobic bioaugmentation of phenolic wastewater: Model optimization and system stabilization

The study optimized the parameters of low-intensity ultrasound (LIUS), including ultrasound density (0.25 W·mL-1), duration (12 min), and interval time (48 h), through a combination of uniform experiments and response surface prediction. The optimized parameters were aimed at enhancing the removal efficiency of phenolic wastewater to approximately 80%. Furthermore, they facilitate the production of hydrolytic gases in anaerobic digestion, resulting in methane accumulation of up to 237.3 mL·(g VS)-1. Following the long-term experiment, LIUS has been demonstrated to effectively enhance the enzyme activity of anaerobic organisms while also damaging the bacterial structure of microorganisms. However, microbiological analysis indicates that the ultrasound-induced screening mechanism effectively increases the relative abundance of dominant bacterial communities. This facilitated the removal of persistent phenolic contaminants and stabilized the balanced development of the overall anaerobic environment. These findings suggest that LIUS can enhance biological activity and improve the anaerobic treatment of phenolic wastewater.

Assessment of antibiotic resistance genes in soils polluted by chemical and technogenic ways with poly-aromatic hydrocarbons and heavy metals

Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.

Characterization and risk assessment of polycyclic aromatic hydrocarbons from the emission of different power generator

Epileptic power supply in Sub-Saharan countries of Africa has warranted the use of power generators as an alternative source of power supply. Exhaust emission from these generators is associated with Polycyclic Aromatic Hydrocarbon (PAHs). Hence, this study focused on the determination of levels of PAHs in the emission of different brands of power generators used in Nigeria. Exhaust emissions of different power generators were sampled using a filter-sorbent sampling system with polyurethane foam (PUF) as an adsorbent material. Analysis of PAHs was carried out using a Gas Chromatograph coupled to a mass selective detector (GC- MS) operated on Electron Ionization (EI) mode. The results showed the ∑ PAHs range 14.91-26.0 μ g m - 3 . Bap was the most abundant of all the compounds with a concentration of 2.6 μ g m - 3 with a range of 2.08-3.07 μ g m - 3 . The Incremental Life Cancer Risk (ILCR) values of all the generator's emission sampled are higher than 10- 4 for both children and adult which indicate a high potential cancer risk from inhalation of emission from these generators while Hazard Quotient (HQ) values from all the power generating set in this study are all above 1 which indicated high associated non-carcinogenic. The study revealed the levels of PAHs associated with the emission of power generators in Nigeria.

Distinct Assembly Patterns of Soil Antibiotic Resistome Revealed by Land-Use Changes over 30 Years

Compared with the ever-growing information about the anthropogenic discharge of nutrients, metals, and antibiotics on the disturbance of antibiotic resistance genes (ARGs), less is known about how the potential natural stressors drive the evolutionary processes of antibiotic resistance. This study examined how soil resistomes evolved and differentiated over 30 years in various land use settings with spatiotemporal homogeneity and minimal human impact. We found that the contents of soil organic carbon, nitrogen, soil microbial biomass, and bioavailable heavy metals, as well as related changes in the antibiotic resistome prevalence including diversity and abundance, declined in the order of grassland > cropland > bareland. Sixty-nine remaining ARGs and 14 mobile genetic elements (MGEs) were shared among three land uses. Multiple factors (i.e., soil properties, heavy metals, bacterial community, and MGEs) contributed to the evolutionary changes of the antibiotic resistome, wherein the resistome profile was dominantly driven by MGEs from both direct and indirect pathways, supported by a partial least-squares path model analysis. Our results suggest that pathways to mitigate ARGs in soils can coincide with land degradation processes, posing a challenge to the common goal of managing our environment sustainably.

Interplay of xenobiotic-degrading and antibiotic-resistant microorganisms among the microbiome found in the air, handrail, and floor of the subway station

Investigating the quality of the subway environment, especially regarding antibiotic resistance genes (ARGs) and xenobiotics, conveys ecological and health impacts. In this study, compositions and relations of microorganisms harboring ARGs and xenobiotic degradation and metabolism genes (XDGs) in the Sukhumvit subway station (MRT-SKV) in Bangkok was assessed by analyzing the taxonomic and genetic diversity of the microbiome in the air and on the surfaces of floor and handrail. The major bacteria in the MRT-SKV (including Moraxella, which was abundant in the bioaerosol and handrail samples, and Staphylococcus, which was abundant in the bioaerosol samples) were found to contain both ARGs and XDGs. The co-abundance correlation network revealed notable relationships among bacteria harboring antibiotic resistance genes (ARGs) and xenobiotic degradation genes (XDGs). Significant associations were observed between ARGs linked to glycopeptide and fluoroquinolone resistance and genes associated with benzoate, styrene, and atrazine degradation pathways, as well as between ARGs related to cephamycin, cephalosporin, and MLS resistance and XDGs associated with the cytochrome P450-dependent drug metabolism pathway. These correlations suggested that selective pressure exerted by certain xenobiotics and antibiotics can simultaneously affect both ARGs and XDGs in the environment and should favor correlations and co-survival among ARG- and XDG-containing bacteria in the environments. The correlations may occur via shared mechanisms of resistance to both xenobiotics and antibiotics. Finally, different correlation pairs were seen in different niches (air, handrail, floor) of the subway environment or different geolocations. Thus, the relationship between ARG and XDG pairs most likely depends on the unique characteristics of the niches and on the prominent types of xenobiotics and antibiotics in the subway environment. The results indicated that interactions and connections between microbial communities can impact how they function. These microorganisms can have profound effects on accumulation of xenobiotics and ARGs in the MRT-SKV.

Surveillance and mitigation of soil pollution through metagenomic approaches

Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.

Heterogeneous Antibiotic Resistance Gene Removal Impedes Evaluation of Constructed Wetlands for Effective Greywater Treatment

Microorganisms carrying antimicrobial resistance genes are often found in greywater. As the reuse of greywater becomes increasingly needed, it is imperative to determine how greywater treatment impacts antimicrobial resistance genes (ARGs). Using qPCR and SmartChip™ qPCR, we characterized ARG patterns in greywater microbial communities before, during, and after treatment by a recirculating vertical flow constructed wetland. In parallel, we examined the impact of greywater-treated irrigation on soil, including the occurrence of emerging micropollutants and the taxonomic and ARG compositions of microbial communities. Most ARGs in raw greywater are removed efficiently during the winter season, while some ARGs in the effluents increase in summer. SmartChip™ qPCR revealed the presence of ARGs, such as tetracycline and beta-lactam resistance genes, in both raw and treated greywater, but most abundantly in the filter bed. It also showed that aminoglycoside and vancomycin gene abundances significantly increased after treatment. In the irrigated soil, the type of water (potable or treated greywater) had no specific impact on the total bacterial abundance (16S rRNA gene). No overlapping ARGs were found between treated greywater and greywater-irrigated soil. This study indicates ARG abundance and richness increased after treatment, possibly due to the concentration effects of the filter beds.

The effects of food provisioning on the gut microbiota community and antibiotic resistance genes of Yunnan snub-nosed monkey

Yunnan snub-nosed monkeys (Rhinopithecus bieti) are the highest elevation lived non-human primate, and their survival has been threatened for decades. To promote their population growth, a reserve provides a typical monkey population with supplemental food. However, the influences of this food provisioning on their gut microbiota and antibiotic resistance genes (ARGs) were unknown. Therefore, we investigated the gut microbiota and ARGs of the food-provisioned monkey population compared with another wild foraging population. We found that food provisioning significantly increased the gut microbiota diversity and changed the community composition, particularly increased both the Firmicutes abundance and Firmicutes/Bacteroidetes ratio. Meanwhile, the food provisioning decreased the complex and stable gut microbiota network. KEGG functions were also influenced by food provisioning, with wild foraging monkeys showing higher functions of metabolism and genetic information processing, especially the carbohydrate metabolism, while food-provisioned monkeys exhibited increased environmental information processing, cellular processes, and organismal systems, including valine, leucine, and isoleucine degradation. In addition, food provisioning increased the abundance of ARGs in the gut microbiota, with most increasing the abundance of bacA gene and changing the correlations between specific ARGs and bacterial phyla in each population. Our study highlights that even food provisioning could promote wildlife nutrient intake, and it is necessary to pay attention to the increased ARGs and potential effects on gut microbiota stability and functions for this human conservation measure.

Effects of repeated afidopyropen treatment on the structure and function of the soil microbial community

Chemical insecticides are the most effective pest control agents. Afidopyropen is a novel insecticide used against sap-sucking insects, such as aphids. However, the effects of repeated afidopyropen application on the structure and function of soil microorganisms remain unknown. In this study, the changes in the enzyme activities, community structure and function, and relative abundance of antibiotic resistance ontology (ARO) of soil microorganisms were investigated during three repeated afidopyropen applications under laboratory conditions at the maximum recommended dosage (M1) and 10 times the M1 (M10). The neutral phosphatase (NPA) and catalase (CAT) activities in the soil were significantly suppressed after afidopyropen treatment. The Simpson diversity index (1/D) and Shannon-Wiener diversity index (H) also decreased in both the M1 and M10 afidopyropen-treated soils, indicating a remarkable decrease in soil microorganism diversity. The average well color development (AWCD) first increased and subsequently recovered to normal levels after the third application of the insecticide, suggesting that afidopyropen application could increase the metabolic activity of soil microorganisms. Metagenomic analysis showed that repeated afidopyropen application in both the M1 and M10 treatment groups altered the community structure of soil microorganisms, albeit in different ways. Furthermore, repeated afidopyropen application significantly increased the relative ARO abundance, especially in the M10 treatment, with the most dominant AROs being adeF, baeS, and IND-6. These findings reveal the effects of excessive afidopyropen application on soil microorganisms and lay an important foundation for the comprehensive evaluation of the impact of this insecticide on the environment.

Impact of biochar on the antibiotic resistome and associated microbial functions in rhizosphere and bulk soil in water-saving and flooding irrigated paddy fields

The addition of biochar in paddies under the condition of water-saving irrigation can simultaneously achieve soil improvement and water conservation, but little is known about the role of these two regulations in mediating the fate of antibiotic resistome in paddy soils. Here, metagenomic analysis was conducted to investigate the effects and intrinsic mechanisms of biochar application and irrigation patterns on propagation of antibiotic resistance genes (ARGs) in paddy soils. The addition of biochar in paddy soil resulted in a reduction of approximately 1.32%-8.01% in the total absolute abundance of ARGs and 0.60%-22.09% in the numbers of ARG subtype. Compared with flooding irrigation, the numbers of detected ARG subtype were reduced by 1.60%-22.90%, but the total absolute abundance of ARGs increased by 0.06%-5.79% in water-saving irrigation paddy soils. Moreover, the combined treatments of flooding irrigation and biochar could significantly reduce the abundance of ARGs in paddy soils. The incremental antibiotic resistance in soil induced by water-saving irrigation was likewise mitigated by the addition of biochar. Correlation analyses indicated that, the differences in soil physicochemical properties under biochar addition or irrigation treatments contributed to the corresponding changes in the abundance of ARGs. Moreover, the variations of microbial community diversity, multidrug efflux abundance and transport system-related genes in paddy soil were also important for mediating the corresponding differences in the abundance of ARGs under the conditions of biochar addition or irrigation treatments. The findings of this study demonstrated the effectiveness of biochar application in mitigating antibiotic resistance in paddy soils. However, it also highlighted a potential concern relating to the elevated antibiotic resistance associated with water-saving irrigation in paddy fields. Consequently, these results contribute to a deeper comprehension of the environmental risks posed by ARGs in paddy soils.

Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains

For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT's competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.

NCRD: A non-redundant comprehensive database for detecting antibiotic resistance genes

Antibiotic resistance genes (ARGs) are emerging pollutants present in various environments. Identifying ARGs has become a growing concern in recent years. Several databases, including the Antibiotic Resistance Genes Database (ARDB), Comprehensive Antibiotic Resistance Database (CARD), and Structured Antibiotic Resistance Genes (SARG), have been applied to detect ARGs. However, these databases have limitations, which hinder the comprehensive profiling of ARGs in environmental samples. To address these issues, we constructed a non-redundant antibiotic resistance genes database (NRD) by consolidating sequences from ARDB, CARD, and SARG. We identified the homologous proteins of NRD from Non-redundant Protein Database (NR) and the Protein DataBank Database (PDB) and clustered them to establish a non-redundant comprehensive antibiotic resistance genes database (NCRD) with similarities of 100% (NCRD100) and 95% (NCRD95). To demonstrate the advantages of NCRD, we compared it with other databases by using metagenome datasets. Results revealed its strong ability in detecting potential ARGs.

Metagenomic investigations on antibiotic resistance and microbial virulence in oil-polluted soils from China

Engine oil spills have been associated with a wide range of human health problems. However, little is known about the effects of petroleum hydrocarbon pollution on soil microbial communities. In this study, three samples were collected from oil-polluted soils (OPS), and one control soil (CS) from Taolin town, China, near the old engine's scrapes was used. The aims of this study were to conduct metagenomic sequencing and subsequently perform resistome and virulome analysis. We also aimed to validate anti-microbial resistance and virulence genes and anti-bacterial sensitivity profiles among the isolates from oil-polluted soils. The OPS microbial community was dominated by bacterial species compared to the control samples which were dominated by metazoans and other organisms. Secondly, the resistosome and virulome analysis showed that ARGs and virulence factors were higher among OPS microbial communities. Antibiotic susceptibility assay and qPCR analysis for ARGs and virulence factors showed that the oil-polluted soil samples had remarkably enhanced expression of these ARGs and some virulence genes. Our study suggests that oil pollution contributes to shifting microbial communities to more resilient types that could survive the toxicity of oil pollution and subsequently become more resilient in terms of higher resistance and virulence potential.

Microbial electron flow promotes naphthalene degradation in anaerobic digestion in the presence of nitrate electron acceptor: Focus on electron flow regulation and microbial interaction succession

Microbial electron flow (MEF) is produced from microbial degradation of organic compounds. Regulating MEF to promote organic pollutants biodegradation such as naphthalene (Nap) is a potential way but remains a lack of theoretical basis. Here, we regulated MEF by adding electron acceptor NO3- to achieve 2.6 times increase of Nap biodegradation with cyclodextrin as co-metabolism carbon source. With the NO3- addition, the genes inhibited by Nap of electron generation significantly up-regulated. Especially, key genes ubiD and nahD for anaerobic Nap degradation significantly up-regulated respectively 3.7 times and 6.7 times. Moreover, the ability of electron transfer in MEF was also improved consistent with 7.2 times increase of electron transfer system (ETS) activity. Furthermore, total 60 metagenome-assembled genomes (MAGs) were reconstructed through the metagenomic sequencing data with assembly and binning strategies. Interestingly, it was also first found that the Klebsiella MAG. SDU (Shandong University) 14 had the ability of simultaneous Nap biodegradation and denitrification. Our results firstly offered an effective method of regulating MEF to promote polycyclic aromatic hydrocarbons (PAHs) degradation and simultaneous methanogenesis.

Regional distribution and migration potential of antibiotic resistance genes in croplands of Qinghai Tibet Plateau

Agricultural activities have recently disturbed the ecosystem of the Qinghai-Tibet Plateau and the shift of antibiotic resistance genes (ARGs) in the different types of farmlands is not well understood, so more comprehensive ecological barrier management measures cannot be provided for the region. This research was performed to exploring ARG pollution in cropland soil on the Qinghai-Tibet Plateau to obtain information on the geographical and climatic factors shaping the ARG distribution. Based on high-throughput quantitative PCR (HT-qPCR) analysis, the ARG abundance in farmland ranged from 5.66 × 105 to 6.22 × 107 copies per gram of soil higher than previous research at soil and wetland in Qinghai-Tibet plateau, and it was higher in wheat and barley soils than in corn soil. The distribution of ARGs exhibited regional features as ARG abundance was adversely affected by mean annual precipitation and temperature with lower temperature and less rainfall at high altitude. According to network analysis and structural equation modeling (SEM), mobile genetic elements (MGEs) and heavy metals are the key drivers of ARG dissemination on the Qinghai-Tibet Plateau as they show negative relationship with ARGs, and selection copressure from heavy metals in cropland soil increases the horizontal gene transfer (HGT) potential of ARGs through synergistic selection effects, each contribution to the ARGs was 19% and 29% respectively. This research suggests the need to focus on controlling heavy metals and MGEs to constrain the dissemination of ARGs, as arable soil is already slightly contaminated by heavy metals.

The dynamics and transmission of antibiotic resistance associated with plant microbiomes

Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.

Unexpected enrichment of antibiotic resistance genes and organic remediation genes in high-altitude lakes at Eastern Tibetan Plateau

Elevation has a strong effect on aquatic microbiome. However, we know little about the effects of elevation on functional genes, especially antibiotic resistance genes (ARGs) and organic remediation genes (ORGs) in freshwater ecosystems. In this study, we analyzed five classes of functional genes including ARGs, metal resistance genes (MRGs), ORGs, bacteriophages, and virulence genes between two high-altitude lakes (HALs) and two low-altitude lakes (LALs) in Mountain Siguniang at Eastern Tibetan Plateau by means of GeoChip 5.0. No differences (Student's t-test, p > 0.05) of gene richness including ARGs, MRGs, ORGs, bacteriophages, and virulence genes in HALs and LALs were found. The abundance of most ARGs and ORGs was higher in HALs than in LALs. For MRGs, the abundance of macro metal resistance genes of potassium, calcium, and aluminum was higher in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d > 0.8). The abundance of some heavy metal resistance genes of lead and mercury was lower in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d < -0.8). The composition of these functional genes in HALs differed significantly from in LALs. The functional gene network in HALs was also more complex than that in LALs. We speculate that enrichment of ARGs and ORGs in HALs is related to different microbial communities, exogenous ARGs, and enriched persistent organic pollutants through long-range atmospheric transport driven by the Indian monsoon. This study highlights the unexpected enrichment of ARGs, MRGs, and ORGs in remote lakes at high elevations.

Deep relationships between bacterial community and polycyclic aromatic hydrocarbons in soil profiles near typical coking plants

Bacterial communities play an important role in maintaining the normal functioning of ecosystems; therefore, it is important to understand the effects of polycyclic aromatic hydrocarbons (PAHs) on the bacterial community. In addition, understanding the metabolic potential of bacterial communities for PAHs is important for the remediation of PAH-contaminated soils. However, the deep relationship between PAHs and bacterial community in coking plants is not clear. In this study, we determined the bacterial community and the concentration of PAHs in three soil profiles contaminated by coke plants in Xiaoyi Coking Park, Shanxi, China, using 16S rRNA and gas chromatography coupled with mass spectrometry, respectively. The results show that 2 ~ 3 rings PAHs are the main PAHs and Acidobacteria (23.76%) was the dominant bacterial community in three soil profiles. Statistical analysis showed that there were significant differences in the composition of bacterial communities at different depths and different sites. Redundancy analysis (RDA) and variance partitioning analysis (VPA) illustrate the influence of environmental factors (including PAHs, soil organic matter (SOM), and pH) on the vertical distribution of soil bacterial community, and PAHs were the main factors affecting the bacterial community in this study. The co-occurrence networks further indicated correlations between bacterial community and PAHs and found that Nap has the greatest effect on bacterial community compared with other PAHs. In addition, some operational taxonomic units (OTUs, OTU2, and OTU37) have the potential to degrade PAHs. PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used for further study on the potential of microbial PAHs degradation from a genetic perspective, which showed that different PAH metabolism genes were present in the genomes of bacterial communities in the three soil profiles, and a total of 12 PAH degradation-related genes were isolated, mainly dioxygenase and dehydrogenase genes.

The antimicrobial resistance profiles of Escherichia coli and Pseudomonas aeruginosa isolated from private groundwater wells in the Republic of Ireland

The role of the natural environment in the dissemination of antimicrobial resistant bacteria has been increasingly recognised in the literature. However, knowledge surrounding the critical factors and mechanisms mediating their occurrence is still limited, particularly in relatively 'pristine' groundwater environments. In the Republic of Ireland (RoI), a country characterised by high groundwater reliance, household-based (unregulated) wells provide drinking water to 11% of the population. These private wells are generally located in rural areas, where the risk of microbiological contamination is high due to intensive agricultural practices and high reliance on domestic wastewater treatment systems; both of which are also potential sources of antimicrobials and antimicrobial resistant bacteria. Accordingly, the current research sought to elucidate current rates of antimicrobial resistant bacteria and the principal factors associated with their presence in private wells in the RoI. A total of 250 samples (from 132 wells nationwide) were assessed for the presence of faecal (Escherichia coli) and environmental (Pseudomonas aeruginosa) bacteria, with single isolates from each contaminated sample tested phenotypically against 18 and 9 antimicrobials, respectively. Findings show that while 16.7% of E. coli (n = 8/48) were categorically resistant to ≥1 antimicrobial, with a further 79.2% classified as intermediately resistant, no categorical resistance was found among P. aeruginosa isolates (n = 0/6), with just one intermediately resistant isolate detected. Multivariate regression modelling indicates significantly higher odds of resistant E. coli detection in concurrence with elevated cattle density (OR = 1.028, p = 0.032), aligning with findings of highest resistance rates to veterinary antimicrobials (e.g., streptomycin = 14.6%, tetracycline = 12.5%, and ampicillin = 12.5%). Multivariate model results also suggest overland flow culminating in direct wellhead ingress as a primary ingress mechanism for resistant E. coli. Study findings may inform groundwater source protection initiatives and antimicrobial resistance surveillance moving forward.

Bioaccessible PAH influence on distribution of antibiotic resistance genes and soil toxicity of different types of land use

For a better understanding of the dissemination of antibiotic resistance genes (ARGs) in natural microbial communities, it is necessary to study the factors influencing it. There are not enough studies showing the connection of some pollutants with the dissemination of ARGs and especially few works on the effect of polycyclic aromatic compounds (PAHs) on the spread of resistance in microbiocenosis. In this respect, the aim of the study was to determine the effect of bioaccessible PAHs on soil resistome. The toxicity and the content of bioaccessible PAHs and ARGs were studied in 64 samples of soils of different types of land use in the Rostov Region of Russia. In most soils, a close positive correlation was demonstrated between different ARGs and bioaccessible PAHs with different content of rings in the structure. Six of the seven studied ARGs correlated with the content of 2-, 3-, 4-, 5- or 6-ring PAHs. The greatest number of close correlations was found between the content of PAHs and ARGs in the soils of protected areas, for agricultural purposes, and in soils of hospitals. The diverse composition of microbial communities in these soils might greatly facilitate this process. A close correlation between various toxic effects identified with a battery of whole-cell bacterial biosensors and bioaccessible PAHs of various compositions was established. This correlation showed possible mechanisms of PAHs' influence on microorganisms (DNA damage, oxidative stress, etc.), which led to a significant increase in horizontal gene transfer and spread of some ARGs in soil microbial communities. All this information, taken together, suggests that bioaccessible PAHs can enhance the spread of antibiotic resistance genes.

Insight into the impacts and mechanisms of ketone stress on the antibiotic resistance in Escherichia coli

Accumulation of toxic organic has posed a substantial pressure on the proliferation of bacterial resistance. While aromatic organics have been demonstrated to enhance the antibiotic resistance in bacteria, no information is yet available on the effects of non-aromatic organics on the variations of bacterial resistance. Here, we investigated the effects of a typical ketone (i.e., methylisobutanone (MIBK)) on the variations of antibiotic resistance in Escherichia coli (E. coli). The results showed that the growth of resistant E. coli under environmental concentration of 50 μg/L MIBK was firstly inhibited as explained by the transient disruption in the cell membrane and then recovered possibly due to the reactive oxygen species. Exposure to 50 μg/L MIBK gradually raised the abundance of representative resistance gene (ampR) in E. coli. In contrast, the high concentration of 50 mg/L MIBK continuously inhibited the growth of resistant E. coli by disrupting cell membrane and notably promoted the proliferation of ampR through enhancing the horizontal transformation and up-regulating the expression of efflux pump gene. These findings provided the first evidence for the evolution of bacterial resistance in response to ketone organics.

Insight into co-hosts of nitrate reduction genes and antibiotic resistance genes in an urban river of the qinghai-tibet plateau

Microbial co-hosts of nitrate reduction genes (NRGs) and antibiotic resistance genes (ARGs) have been recently reported, but their ecology and biochemical role in urban waterways remain largely unknown. Here, we collected 29 surface water and 29 sediment samples in the Huangshui River on the Qinghai-Tibet Plateau during the wet and dry season, and 11 water samples from wastewater treatment plants and wetlands along the river. Using metagenomic sequencing, we retrieved 278 medium-to-high-quality metagenome-assembled genomes (MAGs) of NRG-ARG co-hosts, mainly belonging to the phyla Proteobacteria, Actinobacteriota, and Bacteroidota. Of microorganisms carrying ARGs, a high proportion (75.3%‒94.9%) also encoded NRGs, supporting nitrate reducing bacteria as dominant hosts of ARGs. Seasonal changes in antibiotic levels corresponded to significant variation in the relative abundance of NRG-ARG co-host in both water and sediments, resulting in a concomitant change in antibiotic resistance pathways. In contrast, the contribution of NRG-ARG co-hosts to nitrate reduction was stable between seasons. We identify specific antibiotics (e.g., sulphonamides) and microbial taxa (e.g., Acinetobacter and Hafnia) that may disproportionately impact these relationships to serve as a basis for laboratory investigations into bioremediation strategies. Our study suggests that highly abundant nitrate reducing microorganisms in contaminated environments may also directly impact human health as carriers of antibiotic resistance.

Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments

As sequencing technology improves and the cost of metagenome sequencing decreases, the number of sequenced environments increases. These metagenomes provide a wealth of data in the form of annotated and unannotated genes. The role of multidrug resistance efflux pumps (MDREPs) is the removal of antibiotics, biocides and toxic metabolites created during aromatic hydrocarbon metabolism. Due to their naturally occurring role in hydrocarbon metabolism and their role in biocide tolerance, MDREP genes are of particular importance for the protection of pipeline assets. However, the heterogeneity of MDREP genes creates a challenge during annotation and detection. Here we use a selection of primers designed to target MDREPs in six pure species and apply them to publicly available metagenomes associated with oil and gas environments. Using in silico PCR with relaxed primer binding conditions we probed the metagenomes of a shale reservoir, a heavy oil tailings pond, a civil wastewater treatment, two marine sediments exposed to hydrocarbons following the Deepwater Horizon oil spill and a non-exposed marine sediment to assess the presence and abundance of MDREP genes. Through relaxed primer binding conditions during in silico PCR, the prevalence of MDREPs was determined. The percentage of nucleotide sequences identified by the MDREP primers was partially augmented by exposure to hydrocarbons in marine sediment and in shale reservoir compared to hydrocarbon-free marine sediments while tailings ponds and wastewater had the highest percentages. We believe this approach lays the groundwork for a supervised method of identifying poorly conserved genes within metagenomes.

The source, fate and prospect of antibiotic resistance genes in soil: A review

Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.

Antibiotic resistance in plant growth promoting bacteria: A comprehensive review and future perspectives to mitigate potential gene invasion risks

Plant growth-promoting bacteria (PGPB) are endowed with several attributes that can be beneficial for host plants. They opened myriad doors toward green technology approach to reduce the use of chemical inputs, improve soil fertility, and promote plants' health. However, many of these PGPB harbor antibiotic resistance genes (ARGs). Less attention has been given to multi-resistant bacterial bioinoculants which may transfer their ARGs to native soil microbial communities and other environmental reservoirs including animals, waters, and humans. Therefore, large-scale inoculation of crops by ARGs-harboring bacteria could worsen the evolution and dissemination of antibiotic resistance and aggravate the negative impacts on such ecosystem and ultimately public health. Their introduction into the soil could serve as ARGs invasion which may inter into the food chain. In this review, we underscore the antibiotic resistance of plant-associated bacteria, criticize the lack of consideration for this phenomenon in the screening and application processes, and provide some recommendations as well as a regulation framework relating to the development of bacteria-based biofertilizers to aid maximizing their value and applications in crop improvement while reducing the risks of ARGs invasion.

Influence of site-specific factors on antibiotic resistance in agricultural soils of Yangtze River Delta: An integrated study of multi-factor modeling

Agricultural soils are important reservoirs for antibiotic resistance genes (ARGs), which is closely linked to soil microorganisms. Environmental factors and co-existed pollutants may function as promoters or inhibitors for ARG proliferation to influence the agriculture green development. However, research focusing on the interaction of potential environmental drivers and ARGs is still lacking in agricultural soils. Here, we explored the microbial profile in 241 soil samples in Yangtze River Delta, and analyzed the relationship of microbial structures, ARGs, and typical site-specific factors. We found that the abundance of most ARGs was negatively correlated with the ratio of fungi and bacteria (F/B), whereas positively correlated with the ratio of gram-positive and gram-negative microbes (G⁺/G^-). The co-occurrence network revealed significant associations among 18 site-specific factors, including 6 meteorological factors, 5 soil physicochemical properties, 5 co-existed organic pollutants, and 2 co-existed heavy metals. Random forest analysis demonstrated that F/B was mainly influenced by soil organic matters and co-existed polychlorinated biphenyls, while G⁺/G^- was predominately regulated by soil total phosphorus and moisture content, which possibly resulting in their difference relationship with ARG abundance. Besides, the contribution of meteorological factors (>30%) in the explanation for F/B and G⁺/G^- structures was the highest among all the site-specific factors. Together with path analysis showing meteorological factors probably affecting the ARG abundance through direct positive ways or indirect paths via physicochemical properties, microbial structure, and co-existed organic pollutants, we considered meteorological factors as the potential promoters for ARG proliferation. Collectively, these results increase our understanding of agricultural soils as hotspots of ARGs, and highlight the underappreciated role of meteorological factors as potential promoters for soil ARGs, providing reference for us to regulate ARG pollution scientifically to improve the development of green agriculture.

Tidal flat aquaculture pollution governs sedimentary antibiotic resistance gene profiles but not bacterial community based on metagenomic data

Coastal tidal flats are intersection zones between terrestrial and marine environments and are considered repositories of pollutants from anthropogenic activities (e.g., fishery and aquaculture). Specifically, the prevalence of antibiotics and antibiotic resistance genes (ARGs) in coastal aquaculture environments pose critical threats to estuarine ecosystems. However, the contribution of aquaculture to the occurrence and abundance of ARGs and community assemblies has not been fully explored in tidal flat zones. Thus, we investigated ARGs profiles, ARG-carrying host bacteria, and their associate microbial community in the Dongtai and Sheyang tidal flat aquaculture regions of Jiangsu, China using metagenomic assembly methods. The antibiotic concentrations in the sediment samples ranged from nd to 35.50 ng/g dw, and the antibiotic pollution in the Dongtai tidal flat was more severe than in the Sheyang tidal flats. Metagenomic assembly indicated that a total of 247 ARG subtypes associated with ARG 33 types were characterized across all samples and their abundance in the Dongtai region exceeded that in the Sheyang region. Meanwhile, 21 bacteria in the tidal flat aquaculture were identified as ARG-carrying pathogens, including Escherichia coli, Vibrio fluvialis, and Staphylococcus aureus. Using neutral and null modeling analysis to determine the community ecological processes, the results revealed bacterial and ARG communities were generally dominated by stochastic and deterministic processes, respectively. The above results suggested that aquaculture pollution was contributed to shape ARG profiles in tidal flats. The observed deterministic processes affecting the ARG community in tidal flat aquaculture also provides an effective foundation to control the risks of environmental antibiotic resistance through reducing aquaculture antibiotic usage.

Metagenomic Characterization of Resistance Genes in Deception Island and Their Association with Mobile Genetic Elements

Antibiotic resistance genes (ARGs) are undergoing a remarkably rapid geographic expansion in various ecosystems, including pristine environments such as Antarctica. The study of ARGs and environmental resistance genes (ERGs) mechanisms could provide a better understanding of their origin, evolution, and dissemination in these pristine environments. Here, we describe the diversity of ARGs and ERGs and the importance of mobile genetic elements as a possible mechanism for the dissemination of resistance genes in Antarctica. We analyzed five soil metagenomes from Deception Island in Antarctica. Results showed that detected ARGs are associated with mechanisms such as antibiotic efflux, antibiotic inactivation, and target alteration. On the other hand, resistance to metals, surfactants, and aromatic hydrocarbons were the dominant ERGs. The taxonomy of ARGs showed that Pseudomonas, Psychrobacter, and Staphylococcus could be key taxa for studying antibiotic resistance and environmental resistance to stress in Deception Island. In addition, results showed that ARGs are mainly associated with phage-type mobile elements suggesting a potential role in their dissemination and prevalence. Finally, these results provide valuable information regarding the ARGs and ERGs in Deception Island including the potential contribution of mobile genetic elements to the spread of ARGs and ERGs in one of the least studied Antarctic ecosystems to date.

An Overview of Antibiotic Resistance and Abiotic Stresses Affecting Antimicrobial Resistance in Agricultural Soils

Excessive use of antibiotics in the healthcare sector and livestock farming has amplified antimicrobial resistance (AMR) as a major environmental threat in recent years. Abiotic stresses, including soil salinity and water pollutants, can affect AMR in soils, which in turn reduces the yield and quality of agricultural products. The objective of this study was to investigate the effects of antibiotic resistance and abiotic stresses on antimicrobial resistance in agricultural soils. A systematic review of the peer-reviewed published literature showed that soil contaminants derived from organic and chemical fertilizers, heavy metals, hydrocarbons, and untreated sewage sludge can significantly develop AMR through increasing the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in agricultural soils. Among effective technologies developed to minimize AMR's negative effects, salinity and heat were found to be more influential in lowering ARGs and subsequently AMR. Several strategies to mitigate AMR in agricultural soils and future directions for research on AMR have been discussed, including integrated control of antibiotic usage and primary sources of ARGs. Knowledge of the factors affecting AMR has the potential to develop effective policies and technologies to minimize its adverse impacts.

A meta-analysis reveals that operational parameters influence levels of antibiotic resistance genes during anaerobic digestion of animal manures

Anaerobic digestion (AD) has shown the potential to reduce the numbers and types of antibiotic-resistance genes (ARG) present in animal manures. However, the variability of the results has limited the ability to draw solid conclusions. To address this issue, we performed a series of meta-analyses to evaluate how AD of pig, cattle, and dairy manures affects ARG levels and how different parameters, such as temperature, pH, digestion times, and the addition of other substances (e.g., solids, antibiotics) influence ARG changes. Twenty studies with enough details on changes in ARG levels during the AD process were identified and used for the meta-analyses. The results suggested that AD could significantly reduce ARG levels regardless of the conditions of the process. Also, thermophilic AD was more effective than mesophilic AD at reducing ARGs, although this difference was only significant for pig manures. The results also suggested that long digestion times (>50 days) yielded better ARG reduction rates, and that the addition of solids from an external source (co-digestion) negatively affected the efficiency of ARG reduction. In general, the results suggested that ARG changes during AD could be linked to the abundance and activity of hydrolytic communities.

Distribution and Transfer of Antibiotic Resistance Genes in Coastal Aquatic Ecosystems of Bohai Bay

Antibiotic resistance genes (ARGs) are abundant in diverse ecosystems and the resistome may constitute a health threat for humans and animals. It is necessary to uncover ARGs and the accumulation mechanisms from different environmental sources. Various habitats, such as soil, seawater and fish intestines, could overflow a considerable amount of ARGs and the horizontal transfer of ARGs may occur in these environments. Thus, we assessed the composition and abundance of ARGs in seawater, soil and intestinal tracts of Cynoglossus semilaevis collected from different sites in Bohai Bay (China), including a natural area and three fish farms, through a high-throughput qPCR array. In total, 243 ARGs were uncovered, governing the resistance to aminoglycoside, multidrug, beta-lactamase, macrolide lincosamide streptomycin B (MLSB), chloramphenicol, sulfonamide, tetracycline, vancomycin and other antibiotics. The action mechanisms of these ARGs were mainly antibiotic deactivation, efflux pump and cellular protection. Importantly, similar ARGs were detected in different samples but show dissimilar enrichment levels. ARGs were highly enriched in the fish farms compared to the natural sea area, with more genes detected, while some ARGs were detected only in the natural sea area samples, such as bacA-02, tetL-01 and ampC-06. Regarding sample types, water samples from all locations shared more ARGs in common and held the highest average level of ARGs detected than in the soil and fish samples. Mobile genetic elements (MGEs) were also detected in three sample types, in the same trend as ARGs. This is the first study comparing the resistome of different samples of seawater, soil and intestines of C. semilaevis. This study contributes to a better understanding of ARG dissemination in water sources and could facilitate the effective control of ARG contamination in the aquatic environment.

Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors

Estuaries are resistome hotspots owing to resistome accumulation and propagation at these locations from surrounding rivers, yet the large-scale biogeographic pattern of resistome, especially biocide and metal resistance genes (BMRGs) and its driving mechanisms in estuarine waters remains to be elucidated. Here, a metagenomics-based approach was firstly used to investigate resistome and mobilome profiles in waters from 30 subtropical estuaries, South China. The Pearl River estuaries had a higher diversity and abundance of antibiotic resistance genes (ARGs), BMRGs, and mobile genetic elements (MGEs) when compared with estuaries from east and west regions. Genes resistant to multiple antibiotics, metals, and biocides were the most abundant gene types in the resistome. The abundance of MGEs (e.g., intI1, IS91, and tnpA) was highly associated with the total abundance of resistance genes, suggesting their utility as potential indicators for quantitative estimations of the resistome contamination. Further, MGEs contributed more than bacterial communities in shaping the resistome in subtropical estuaries. Physicochemical factors (e.g., pH) regulated MGE composition and stochastic assembly, which mediated the co-selection of ARGs and BMRGs via horizontal gene transfer. Our findings have important implications and provide a reference on the management of ARGs and BMRGs in subtropical estuarine ecosystems.

Enhanced bioremediation of sediment contaminated with polycyclic aromatic hydrocarbons by combined stimulation with sodium acetate/phthalic acid

In this study, four groups of laboratory scale experiments were performed by adding sodium acetate (SA), phthalic acid (PA), and SA-PA to river sediment to observe the microbial response and biodegradation efficiency of polycyclic aromatic hydrocarbons (PAHs). The results showed that the amount of total organic carbon consumed and the amount of sulfate reduction were both positively correlated (p < 0.01) with the biodegradation efficiency of the sum (∑) PAHs (∼40.5%). The lower the number of rings, the more PAHs were biodegraded, with an efficiency of 63.0% for ∑ (2 + 3) ring PAHs. Based on high-throughput sequencing and molecular ecological network analysis, it was found that the combined stimulation of SA and PA not only increased the relative abundance of PAHs-degrading bacterial (eg., Proteobacteria, Desulfobacterota, Campilobacterota and Firmicutes), but also had a strengthening effect on microbes in sediments. The altered microbial structure caused a variation in metabolic functions, which increased the amino acid metabolism to 12.2%, thus increasing the positive correlations among genera and improving the connectivity of the microbial network (p < 0.01). These changes may be responsible for the enhanced biodegradation of PAHs under SA-PA dosing in comparison to SA or PA dosing alone. This study revealed that the microbial community was stimulated by the combined addition of SA and PA, and indicated its role in enhancing biodegradation of PAHs in contaminated river sediments.

Metagenomic assembly deciphered the type-dependent effects of surfactants on the fates of antibiotics resistance genes during sludge fermentation and the underlying mechanisms

Waste activated sludge (WAS) is an important reservoir of antibiotic resistance genes (ARGs). However, the interactive effects of co-existed substances in WAS on ARGs fates have yet to be disclosed. This study demonstrated the type-dependent effects of surfactants (potentially effective chemicals for WAS disposal) on the reduction of ARGs during WAS fermentation, which followed the order of linear alkylbenzene sulphonates (LAS) > alkyl polyglucoside (APG) > hexadecyl trimethyl ammonium bromide (HTAB). Interestingly, the ratio of ARGs affiliated to efflux pump showed an upward trend in the surfactant-treated reactor. Mechanistic investigations revealed that the extracellular polymeric substances (EPS) destruction induced by surfactants increased the permeability of bacterial cells and caused the ARGs being released and susceptible for subsequent elimination. Besides, the surfactants significantly altered the microbial community, resulting in the ARGs reduction via changing the potential hosts. Also, the metabolic pathways participated in the dissemination of ARGs were remarkably down-regulated, thereby resulting in the reduction of ARGs abundances. This work broadened the understanding of ARGs fates during WAS fermentation and provided insights on the interactive functions of exogenous chemicals in multiple matrics.

Bloom of tetracycline resistance genes in mudflats following fertilization is attributed to the increases in the shared potential hosts between soil and organic fertilizers

A field experiment was carried out in mudflats adjacent to the Yellow Sea, China, amended with sewage sludge and vermicompost by one-time input at different rates to reveal the fates of tetracycline resistance genes (TRGs) and their potential hosts in the soils. Quantitative PCR results showed that soils added with either sludge or vermicompost had more abundant TRGs compared with the non-fertilized soil. This situation was more obvious in sludge fertilized soils especially at high application rates. Vermicompost exhibited a promising outlook for improvement of the mudflats. The abundances of intI1 in the non-fertilized soils were significantly higher than those in fertilizers and fertilized soils. The potential hosts for intI1 were not shared with other TRGs-contained hosts, indicating that intI1 had little effects on the dissemination of TRGs in the mudflats. Moreover, the exclusive hosts for TRGs in fertilizers were not higher than those in the non-fertilized soils, illustrating little effects of fertilization on the introduction of exogenous TRGs into soil. The shared hosts between soil and fertilizers were highest among four possible sources, contributing vastly to the bloom of TRGs following fertilization. It was also shown that different organic fertilizers caused distinct categories of shared potential hosts for TRGs. RDA analysis further indicated that the abundances of the shared potential hosts were affected by soil nutrients. These results suggested that the development of TRGs in soil following fertilization depended on the shared potential hosts with similar ecological niches between soil and fertilizers.

Ecological selection of bacterial taxa with larger genome sizes in response to polycyclic aromatic hydrocarbons stress

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous priority pollutants that cause great damage to the natural environment and health. Average genome size in a community is critical for shedding light on microbiome's functional response to pollution stress within an environment. Here, microcosms under different concentrations were performed to evaluate the selection of PAHs stress on the average genome size in a community. We found the distinct communities of significantly larger genome size with the increase of PAHs concentration gradients in soils, and consistent trends were discovered in soils at different latitudes. The abundance of Proteobacteria and Deinococcus-Thermus with relatively larger genomes increased along with PAHs stress and well adapted to polluted environments. In contrast, the abundance of Patescibacteria with a highly streamlined and smaller genome decreased, implying complex interactions between environmental selection and functional fitness resulted in bacteria with larger genomes becoming more abundant. Moreover, we confirmed the increased capacity for horizontal transfer of degrading genes between communities by showing an increased connection number per node positively related to the nidA gene along the concentration gradients in the co-occurrence network. Our findings suggest PAHs tend to select bacterial taxa with larger genome sizes, with significant consequences for community stability and potential biodegradation strategies.

Phenolic compounds promote the horizontal transfer of antibiotic resistance genes in activated sludge

Phenolic compounds are common organic pollutants in wastewater. During the wastewater treatment process, these compounds may influence the microbial community structure and functions. However, the impact of the phenolic compounds in the wastewater treatment plants on the horizontal transfer of antibiotic resistance genes (ARGs) has not been well assessed. In this study, we investigated the horizontal transfer of ARGs under the stress of phenolic compounds. The results showed that in pure culture bacteria system, p-nitrophenol (PNP), p-aminophenol (PAP) and phenol (PhOH) (10-100 mg/L) can significantly increase the horizontal transfer frequency of ARGs by 2.2-4.6, 3.6-9.4 and 1.9-9.0 fold, respectively. And, the RP4 plasmid transfer from Escherichia coli HB101 (E. coli HB101) to the bacteria in activated sludge increased obviously under the stress of phenolic compounds. Further investigation revealed that the PNP and PhOH at the concentration of 10-100 mg/L increased the production of reactive oxygen species and the permeability of cell membrane in the donor and recipient, which could be the causes of horizontal transfer of RP4 plasmid. In addition, it was also found that PNP, PAP and PhOH stress inhibit the expression of the global regulatory genes korB and trbA in the RP4 plasmid, and increase the expression level of the traF gene, thereby promoting the conjugative transfer of the RP4 plasmid. Taken together, these results improved our understanding of the horizontal transfer of ARGs under the stress of phenolic compounds and provided basic information for management of the systems that treat wastewater containing phenolic compounds.

Development of an Autochthonous Microbial Consortium for Enhanced Bioremediation of PAH-Contaminated Soil

The main objectives of this study were to isolate bacteria from soil chronically contaminated with polycyclic aromatic hydrocarbons (PAHs), develop an autochthonous microbial consortium, and evaluate its ability to degrade PAHs in their native contaminated soil. Strains with the best bioremediation potential were selected during the multi-stage isolation process. Moreover, to choose bacteria with the highest bioremediation potential, the presence of PAH-degrading genes (pahE) was confirmed and the following tests were performed: tolerance to heavy metals, antagonistic behavior, phytotoxicity, and antimicrobial susceptibility. In vitro degradation of hydrocarbons led to the reduction of the total PAH content by 93.5% after the first day of incubation and by 99.22% after the eighth day. Bioremediation experiment conducted in situ in the contaminated area resulted in the average reduction of the total PAH concentration by 33.3% after 5 months and by over 72% after 13 months, compared to the concentration recorded before the intervention. Therefore, this study implicates that the development of an autochthonous microbial consortium isolated from long-term PAH-contaminated soil has the potential to enhance the bioremediation process.

Legacy and Emerging Pollutants in an Urban River Stretch and Effects on the Bacterioplankton Community

River contamination is due to a chemical mixture of point and diffuse pollution, which can compromise water quality. Polycyclic Aromatic Hydrocarbons (PAHs) and emerging compounds such as pharmaceuticals and antibiotics are frequently found in rivers flowing through big cities. This work evaluated the presence of fifteen priority PAHs, eight pharmaceuticals including the antibiotics ciprofloxacin (CIP) and sulfamethoxazole (SMX), together with their main antibiotic resistant genes (ARGs) and the structure of the natural bacterioplankton community, in an urbanized stretch of the river Danube. SMX and diclofenac were the most abundant chemicals found (up to 20 ng/L). ARGs were also found to be detected as ubiquitous contaminants. A principal component analysis of the overall microbiological and chemical data revealed which contaminants were correlated with the presence of certain bacterial groups. The highest concentrations of naphthalene were associated with Deltaproteobacteria and intI1 gene. Overall, the most contaminated site was inside the city and located immediately downstream of a wastewater treatment plant. However, both the sampling points before the river reached the city and in its southern suburban area were still affected by emerging and legacy contamination. The diffuse presence of antibiotics and ARGs causes particular concern because the river water is used for drinking purposes.

Responses of sediment resistome, virulence factors and potential pathogens to decades of antibiotics pollution in a shrimp aquafarm

Aquaculture ecosystem has become a hotspot of antibiotics resistance genes (ARGs) dissemination, owing to the abuse of prophylactic antibiotics. However, it is still unclear how and to what extent ARGs respond to the increasing antibiotic pollution, a trend as expected and as has occurred. Herein, a significant sediment antibiotic pollution gradient was detected along a drainage ditch after decades of shrimp aquaculture. The increasing antibiotic pollution evidently promoted the diversities and tailored the community structures of ARGs, mobile genetic elements (MGEs), virulence factors and pathogens. The profiles of ARGs and MGEs were directly altered by the concentrations of terramycin and sulphadimidine. By contrast, virulence factors were primarily affected by nutrient variables in sediment. The pathogens potentially hosted diverse virulence factors and ARGs. More than half of the detected ARGs subtypes non-linearly responded to increasing antibiotic pollution, as supported by significant tipping points. However, we screened seven antibiotic concentration discriminatory ARGs that could serve as independent variable for quantitatively diagnosing total antibiotic concentration. Co-occurrence analysis depicted that notorious aquaculture pathogens of Vibrio harveyi and V. parahaemolyticus potentially hosted ARGs that confer resistance to multiple antibiotics, while priority pathogens for humankind, e.g., Helicobacter pylori and Staphylococcus aureus, could have harbored redundant virulence factors. Collectively, the significant tipping points and antibiotic concentration-discriminatory ARGs may translate into warning index and diagnostic approach for diagnosing antibiotic pollution. Our findings provided novel insights into the interplay among ARGs, MGEs, pathogens, virulence factors and geochemical variables under the scenario of increasing antibiotic pollution.