Deciphering the transfers of antibiotic resistance genes under antibiotic exposure conditions: Driven by functional modules and bacterial community

Molecular ecological insights into the synergistic response mechanism of nitrogen transformation, electron flow and antibiotic resistance genes in aerobic activated sludge systems driven by sulfamethoxazole and/or trimethoprim stresses

The prevalence of antibiotics poses a serious challenge to biological nitrogen removal in wastewater. In this study, the effects of sulfamethoxazole and/or trimethoprim (15 mg/L∼30 mg/L) on treatment performance, nitrogen transformation and antibiotic resistance genes (ARGs) were investigated in aerobic activated sludge systems to elucidate the metabolic mechanism under high antibiotic stress. 15 mg/L single antibiotic stress improved total nitrogen removal performance due to the persistence of nitrifiers and enrichment of denitrifiers, with an optimum removal efficiency of 96.5 %. Up-regulation of all denitrifying genes, coupled with enhanced electron transfer of Complex II and III, contributed to the emergence of aerobic denitrification. The increased expression of antioxidant genes also alleviated intracellular pressure. Whereas combined antibiotic stress induced the significant down-regulation of denitrifying bacteria and genes (nirKS and nosZ), and suppressed the electron supply for denitrification by restraining genes related to Complex Ⅰ and energy supply by tricarboxylic acid cycle, driving the collapse of activated sludge system, with ammonia and total nitrogen removal efficiencies dropping to below 40 % and 20 %, respectively. The dominant genera in system changed from TM7a to Thiothrix and Sphaerotilus with increasing antibiotic concentration and type. Moreover, antibiotic stress promoted a slight enrichment of ARGs, especially those encoding efflux mechanisms. Cooperative relationships (> 93 %) dominated among ARGs, and Klebsiella was identified as the crucial host. ARGs regulating antibiotic efflux were more likely to be co-expressed with functional genes. These results may provide a theoretical basis for establishing promising strategies to mitigate antibiotic-caused process deterioration.

Removal of ofloxacin and inhibition of antibiotic resistance gene spread during the aerobic biofilm treatment of rural domestic sewage through the micro-nano aeration technology

Micro-nano aeration (MNA) has great potential for emerging contaminant removal. However, the mechanism of antibiotic removal and antibiotic resistance gene (ARG) spread, and the impact of the different aeration conditions remain unclear. This study investigated the adsorption and biodegradation of ofloxacin (OFL) and the spread of ARGs in aerobic biofilm systems under MNA and conventional aeration (CVA) conditions. Results showed that the MNA increased OFL removal by 17.27 %-40.54 % and decreased total ARG abundance by 36.37 %-54.98 %, compared with CVA. MNA-induced biofilm rough morphology, high zeta potential, and reduced extracellular polymeric substance (EPS) secretion enhanced OFL adsorption. High dissolved oxygen and temperature, induced by MNA-enriched aerobic bacteria and their carrying OFL-degrading genes, enhanced OFL biodegradation. MNA inhibited the enrichment of ARG host bacteria, which acquired ARGs possibly via horizontal gene transfer (HGT). Functional profiles involved in the HGT process, including reactive oxygen species production, membrane permeability, mobile genetic elements (MGEs), adenosine triphosphate synthesis, and EPS secretion, were down-regulated by MNA, inhibiting ARG spread. Partial least-squares path modeling revealed that MGEs might be the main factor inhibiting ARG spread. This study provides insights into the mechanisms by which MNA enhances antibiotic removal and inhibits ARG spread in aerobic biofilm systems.

Dissemination mechanisms of unique antibiotic resistance genes from flowback water to soil revealed by combined Illumina and Nanopore sequencing

As a byproduct of shale gas extraction, flowback water (FW) is produced in large quantities globally. Due to the unique interactions between pollutants and microorganisms, FW always harbor multiple antibiotic resistance genes (ARGs) that have been confirmed in our previous findings, potentially serving as a point source for ARGs released into the environment. However, whether ARGs in FW can disseminate or integrate into the environmental resistome remains unclear. In this study, unique ARGs from FW were identified, and the ARG profiles in soil and FW-spiked soil were compared using a combination of Illumina and Nanopore sequencing. The results indicated that the total abundance of the soil resistome increased by 30.8 % in soil contaminated with FW. Of this increase, 11.1 % was attributable to the integration of exogenous ARGs from FW into the soil resistome. Sequence alignment at the gene level further confirmed the successful integration of 20 unique ARG sequences classified as multidrug and vancomycin resistance genes into the soil resistome. These 20 ARG sequences were detected only in the FW. Multiple lines of evidence indicated that horizontal gene transfer dominated ARG dissemination in soil contaminated by FW. This conclusion is supported by the discrepancy between changes in mobile ARGs and host abundance, the upregulation of oxidative stress-related genes (SOD1 and SOD2) and the SOS response (lexA and recA), as well as the upregulation of genes related to quorum sensing (virD4, virB9, and virB3) and naked DNA uptake (pilD, pilT, and pilQ).

Metagenomic insight into the enrichment of antibiotic resistance genes in activated sludge upon exposure to nanoplastics

Activated sludge is an important reservoir for the co-occurring emerging contaminants including nanoplastics (NPs) and antibiotic resistance genes (ARGs). However, the impacts and potential mechanisms of NPs on the fate of ARGs in activated sludge are not fully understood. Herein, we used metagenomic approach to investigate the responses of ARGs, host bacteria, mobile genetic elements (MGEs), and functional genes to polystyrene (PS) NPs at environmentally relevant (0.5 mg/L) and high stress concentrations (50 mg/L) in activated sludge. The results showed that 0.5 and 50 mg/L PS NPs increased the relative abundance of ARGs in the activated sludge by 58.68% and 46.52%, respectively (p < 0.05). Host tracking analysis elucidated that the hosts of ARGs were significantly enriched by PS NPs (p < 0.05), with Proteobacteria being the predominant host bacteria. Additionally, the occurrence of new ARGs hosts and the enrichment of MGEs and functional genes (i.e., genes related to SOS response, cell membrane permeability, and secretion system, etc.) indicated that PS NPs promoted horizontal gene transfer (HGT) of ARGs. Finally, path modeling analysis revealed that the proliferation of ARGs caused by PS NPs was primarily attributed to the enhancement of HGT and the enrichment of host bacteria. Our findings contribute to a comprehensive understanding of the spread risk of ARGs in activated sludge under NPs pollution.

A comprehensive review of antibiotics stress on anammox systems: Mechanisms, applications, and challenges

Anaerobic ammonia oxidation (anammox), an energy-efficient technology for treating ammonium-rich wastewater, faces the challenge of antibiotic stress in sewage. This paper systematically evaluated the impact of antibiotics on anammox by considering both inhibitory effects and recovery duration. This review focused on cellular responses, including extracellular polymeric substances (EPS), quorum sensing (QS), and enzymes. Then, the physiological properties of cells and the interactions between nitrogen and carbon metabolism under antibiotic stress were discussed, particularly within the anammoxosome. The microbial community evolution and the development and transfer of antibiotic resistance genes (ARGs) were further analyzed to reveal the resistance mechanisms of anammox. To address the limitations imposed by antibiotics, the development of bio-augmentation and combined processes based on molecular biology techniques, such as bio-electrochemical systems (BES), has been suggested. This review offered new insights into the mechanisms of antibiotic inhibition during the anammox process and aimed to advance their engineering applications.

Evolution of the Black solider fly larvae gut antibiotic resistome during kitchen waste disposal

Kitchen waste (KW) is an important reservoir of antibiotic resistance genes (ARGs). Black solider fly larvae (BSFL) are extensively employed in KW disposal, closely linking to their robust gut microbes. However, antibiotic resistome in BSFL gut during the KW disposal processes and the mechanism remain unclear. In the present study, the antibiotic resistome in BSFL gut within the 12 days KW disposal processes were investigated. Results showed that, ARGs abundance initially increased and subsequently decreased, the five most prevalent core ARG classes were tetracycline, aminoglycoside, cephalosporin, lincosamide and multidrug. A total of 7 MGE types were observed and the horizontal gene transfer (HGT) of ARGs was predominantly mediated by plasmids. Host microbes were mainly categorized into Proteobacteria (98.12 %) and their assemblies were mainly classified into the deterministic processes. To elucidate the driving mechanisms, the mantel test and the structural equation model (SEM) were developed. Results indicated that microbial functions (0.912, p < 0.0001) and microbial community (1.014, p = 0.036), consistently showed very significant relationships with the patterns of ARGs, which presented higher direct effects than indirect effects. Overall, this study makes an initial contribution to a more deepgoing comprehension of the gut antibiotic resistome of BSFL during KW disposal.

Response of sedimentary microbial community and antibiotic resistance genes to aged Micro(Nano)plastics exposure under high hydrostatic pressure

Several studies reported that the presence of microplastics (MPs)/nanoplastics (NPs) in marine environments can alter microbial community and function. Yet, the impact of aged MPs/NPs on deep sea sedimentary ecosystems under high hydrostatic pressure remains insufficiently explored. Herein, the sedimentary microbial community composition, co-occurrence network, assembly, and transfer of antibiotic resistance genes (ARGs) in response to aged MPs/NPs were investigated. Compared with the control, NPs addition significantly reduced bacterial alpha diversity (p < 0.05), whereas MPs showed no significant impact (p > 0.05). Moreover, networks under NPs exhibited decreased complexity than that under MPs and the control, including edges, average degree, and the number of keystone. The assembly of the microbial community was primarily governed by stochastic processes, and aged MPs/NPs increased the importance of stochastic processes. Moreover, exposure to MPs/NPs for one month decreased the abundance of antibiotic resistance genes (ARGs) (from 94.8 to 36.2 TPM), while exposure for four months increased the abundance (from 40.6 to 88.1 TPM), and the shift of ARGs in sediment was driven by both functional modules and microbial community. This study is crucial for understanding the stress imposed by aged MPs/NPs on sedimentary ecosystems under high hydrostatic pressure.

High-generation tetracyclines shifted microbial community composition and induced the emergence of antibiotic resistant bacteria in soil

Tetracyclines (TCs) have been widely detected in agricultural soil due to their widespread use in animal husbandry. The impact of low-generation TCs, i.e., the first- and second- generations, on soil ecosystem has attracted widespread attention. However, the dynamic response of soil microbial community to high-generation TCs, i.e., the third- and fourth- generations, remains largely unknown. Herein, we characterized the variations in the composition, diversity and succession of microbial community and the proliferation of antibiotic resistance genes (ARGs) under the stress of four generations of TCs in brown soil and red soil. The results demonstrated that the exposure of low- and high- generation TCs consistently decreased the alpha diversity and stimulated the succession rate of microbial community in soil. High-generation TCs strongly shifted microbial community composition by reducing community resilience. The complexity of microbial networks and cross-module associations were strengthened to cope with the stress of high-generation TCs in soil. The abundance of ARGs was exacerbated by 1.75 times in response to the fourth-generation TCs compared to control in brown soil. The potential bacterial hosts of ARGs were more diverse in brown soil exposed to high-generation TCs, but the dominant hosts were not changed. These results highlight the potential ecological risk of the newly developed antibiotics, which is helpful for a comprehensive risk assessment of emerging contaminants.

Antibiotic Resistance in Vibrio Bacteria Associated with Red Spotting Disease in Sea Urchin Tripneustes gratilla (Echinodermata)

The red spotting disease harms sea urchins to the extent of mass mortality in the ocean and echinocultures, accompanied by environmental damage and economic losses. The current study emphasizes the antimicrobial resistance of three isolated bacteria, closely related to Vibrio harveyi, Vibrio owensii, and Vibrio fortis, associated with red spotting in the cultured sea urchin Tripneustes gratilla. In vitro trials examined the susceptibility of these bacterial isolates to various antibiotics. In addition, using an in silico examination, we revealed the arsenal of antimicrobial resistance genes in available genomes of various pathogenic Vibrio associated with diseases in sea urchins, fish, shellfish, and corals. These two approaches enabled the discussion of the similarities and differences between aquatic pathogenic Vibrio and their antibiotic resistance. Among them, we revealed a core resistance to tetracyclines and penams by the in vitro examined strains. At the same time, the in silico study also supported this core resistance by the presence of the adeF and CRP genes in the bacterial genomes. Nevertheless, variability and specific resistance were evident at the species and strain levels in the Vibrio bacteria and genomes. The in vitro trials highlighted the diverse resistance of the Vibrio harveyi-like isolate to all examined antibiotics, while the other two isolates were found susceptible to nitrofurantoin and sulfamethoxazole. The resistance of the Vibrio harveyi-like isolate could not have been obtained in the genome of the proposed relative of Vibrio harveyi VHJR7 that lacks the oqxA and oqxB genes, which enables such a resistance. A unique sensitivity of the Vibrio fortis-like isolate to erythromycin is proposed when compared to other isolated Vibrio and Vibrio genomes that seem capable of resisting this drug. According to the results, we propose nitrofurantoin or sulfamethoxazole for treating two of the red-spotting-associated isolates (Vibrio fortis and Vibrio owensii-like), but not Vibrio harveyi-like. We assume that a shared resistance to some antibiotics by Vibrios is gained by a horizontal gene transfer while previous exposures of a bacterial strain to a specific drug may induce the development of a unique resistance. Finally, we discuss the novel knowledge on antibiotic resistance in Vibrio from the current research in light of the potential risks when using drugs for disease control in aquaculture.

Key role of NH4+-N in the removal of oxacillin during managed aquifer recharge: Reconsidering the recharge limitation

Frequent occurrence of trace antibiotics in reclaimed water is concerning, which inevitably causes aquifer contamination in the case of managed aquifer recharge (MAR). Global governments have formulated strict reclaimed water standards to ensure the safety of water reuse. Recent studies have found that improved antibiotics removal is intimately associated with high ammonia-oxidizing activity. However, the role of NH4+-N in the removal of residual antibiotics of reclaimed water during MAR remains unknown. NH4+-N removal and the effects of ammonia oxidation on antibiotics biodegradation in the aquifer are the most significant facts for solving the above collision. In this work, the effects of NH4+-N (0, 1 and 5 mg/L) in a model refractory antibiotic (oxacillin (OXA), 100 μg/L) attenuation were deciphered by employing three individual simulated MAR columns, which so called N0, N1 and N5. The results showed that 5 mg/L NH4+-N in influent upregulated the abundance of amo genes by 28.9 %-68.0 % in N5. And the enriched functional genes encoding key degradation enzymes enhanced the OXA removal by 18.7 % and alleviated the oxidative stress caused by antibiotics. Subsequently, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) and human bacterial pathogens (HBPs) abundance were all significantly decreased. Moreover, the intimate association between ammonia-oxidizing microorganisms (AOM) and candidate OXA degraders based on microbial network analysis further supported the significance of AOM on OXA biodegradation. This study provides comprehensive evidence that appropriate amounts of NH4+-N are beneficial in antibiotics and antibiotic resistance risk reduction, providing compelling insights for refine NH4+-N recharge limitation.

The variation of resistome, mobilome and pathogen in domestic and industrial wastewater treatment systems

Wastewater treatment plants (WWTPs), including both domestic and industrial facilities, are key contributors to antibiotic resistance genes (ARGs) and human pathogens in the environment. However, the characteristics and dissemination mechanisms of ARGs in domestic (SD) and industrial (SI) wastewater treatment systems remain unclear, leading to uncertainties in risk assessment. Based on metagenomic analysis, we observed significant differences in the compositions of resistome (ARGs and metal resistance genes, MRGs), mobilome (mobile genetic elements, MGEs), and bacterial community between SD and SI. SI exhibited lower diversity of ARGs but higher abundance of MRGs compared to SD. The removal efficiency of resistome was lower in the SI than that in the SD. MGEs emerged as the primary driver of ARG dissemination in the WWTPs, followed by the bacterial community. Environmental conditions (physicochemical parameters, heavy metals, and antibiotics) indirectly influenced the variation of resistome. Significantly, environmental conditions and MGEs highly influenced the composition of resistome in the SI, while bacterial community more associated with resistome in the SD. Additionally, we identified 36 human bacterial pathogens as potential hosts of ARGs, MRGs, and MGEs in wastewater samples. This study provides new insights on the dissemination mechanisms and risk assessment of antimicrobial resistance in the different types of WWTPs.

Microalgae Enhances the Adaptability of Epiphytic Bacteria to Sulfamethoxazole Stress and Proliferation of Antibiotic Resistance Genes Mediated by Integron

The transmission of ARGs in the microalgae-associated epiphytic bacteria remains unclear under antibiotic exposure, apart from altering the microbial community structure. In this study, Chlorella vulgaris cocultured with bacteria screened from surface water was examined to explore the spread of ARGs in the presence of sulfamethoxazole (SMX). The extracellular polymers released by Chlorella vulgaris could reduce antibiotic-induced collateral damage to bacteria, thus increasing the diversity of the microalgae-associated epiphytic bacteria. The abundances of sul1 and intI1 in the phycosphere at 1 mg/L SMX dose increased by 290 and 28 times, respectively. Metagenomic sequencing further confirmed that SMX bioaccumulation stimulated the horizontal transfer of sul1 mediated by intI1 in the microalgae-associated epiphytic bacteria, while reactive oxygen species (ROS)-mediated oxidative stress induced the SOS response and thus enhanced the transformation of sul1 in the J group. This is the first study to verify that microalgae protect bacteria from antibiotic damage and hinder the spread of ARGs mediated by SOS response, while the transfer of ARGs mediated by integron is promoted due to the bioaccumulation of SMX in the phycosphere. The results contribute to present comprehensive understanding of the risk of ARG proliferation by the presence of emerging contaminants residues in river.

Double-edged sword effects of sulfate reduction process in sulfur autotrophic denitrification system: Accelerating nitrogen removal and promoting antibiotic resistance genes spread

This study proposed the double-edged sword effects of sulfate reduction process on nitrogen removal and antibiotic resistance genes (ARGs) transmission in sulfur autotrophic denitrification system. Excitation-emission matrix-parallel factor analysis identified the protein-like fraction in soluble microbial products as main endogenous organic matter driving the sulfate reduction process. The resultant sulfide tended to serve as bacterial modulators, augmenting electron transfer processes and mitigating oxidative stress, thereby enhancing sulfur oxidizing bacteria (SOB) activity, rather than extra electron donors. The cooperation between SOB and heterotroph (sulfate reducing bacteria (SRB) and heterotrophic denitrification bacteria (HDB)) were responsible for advanced nitrogen removal, facilitated by multiple metabolic pathways including denitrification, sulfur oxidation, and sulfate reduction. However, SRB and HDB were potential ARGs hosts and assimilatory sulfate reduction pathway positively contributed to ARGs spread. Overall, the sulfate reduction process in sulfur autotrophic denitrification system boosted nitrogen removal process, but also increased the risk of ARGs transmission.

Preference and regulation mechanism mediated via mobile genetic elements for antibiotic and metal resistomes during composting amended with nano ZVI loaded on biochar

This study assessed the effectiveness of nano zero-valent iron loaded on biochar (BC-nZVI) during swine manure composting. BC-nZVI significantly reduced the abundance of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs). BC-nZVI modified the preference of MGEs to carry ARGs and MRGs, and the corrosion products of BC-nZVI could destroy cell structure, hinder electron transfer between cells, and weaken the association between ARGs, MRGs, and host bacteria. Functional genes analysis revealed that BC-nZVI down-regulated the abundance of genes affecting the transmission and metabolism of ARGs and MRGs, including type IV secretion systems, transporter systems, two-component systems, and multidrug efflux pumps. Furthermore, the BC-nZVI decreased genes related to flagella and pili production and cell membrane permeability, thereby hindering the transfer of ARGs, MRGs, and MGEs in the environment. Redundancy analysis demonstrated that changes in the microbial community induced by BC-nZVI were pivotal factors impacting the abundance of ARGs, MRGs, and MGEs. Overall, this study confirmed the efficacy of BC-nZVI in reducing resistance genes during swine manure composting, offering a promising environmental strategy to mitigate the dissemination of these contaminants.

How micro-/nano-plastics influence the horizontal transfer of antibiotic resistance genes - A review

Plastic debris such as microplastics (MPs) and nanoplastics (NPTs), along with antibiotic resistance genes (ARGs), are pervasive in the environment and are recognized as significant global health and ecological concerns. Micro-/nano-plastics (MNPs) have been demonstrated to favor the spread of ARGs by enhancing the frequency of horizontal gene transfer (HGT) through various pathways. This paper comprehensively and systematically reviews the current study with focus on the influence of plastics on the HGT of ARGs. The critical role of MNPs in the HGT of ARGs has been well illustrated in sewage sludge, livestock farms, constructed wetlands and landfill leachate. A summary of the performed HGT assay and the underlying mechanism of plastic-mediated transfer of ARGs is presented in the paper. MNPs could facilitate or inhibit HGT of ARGs, and their effects depend on the type, size, and concentration. This review provides a comprehensive insight into the effects of MNPs on the HGT of ARGs, and offers suggestions for further study. Further research should attempt to develop a standard HGT assay and focus on investigating the impact of different plastics, including the oligomers they released, under real environmental conditions on the HGT of ARGs.

Parachlorometaxylenol stress caused multidrug-type antibiotic resistance genes proliferation via simultaneously reshaping microbial community and interfering metabolic traits during wastewater treatment process

Despite biological wastewater treatment processes (e.g., sequencing batch reactors (SBR)) being able to reduce the dissemination of antibiotic resistance genes (ARGs), the variation of ARGs under exogenous pollutant stress is an open question. This work investigated the impacts of para-chloro-meta-xylenol (PCMX, typical antibacterial contaminants) on ARGs spread in long-term SBR operation. Although the SBR process inherently decreased ARGs abundance, the presence of PCMX substantially amplified both the prevalence (mainly multidrug) and abundance of total ARGs (1.17-fold of the control). Further analysis demonstrated that PCMX disintegrated sludge structures as well as increased membrane permeability, facilitating the release of mobile genetic elements and subsequent horizontal transfer of ARGs. In addition, PCMX selectively enriched potential ARG hosts, notably Nitrospira and Candidatus Accumulibacter, which predominantly served as multidrug ARG hosts. Concurrently, the self-adaptive functions of ARGs hosts in the PCMX-exposed SBR system were activated via quorum sensing, two-component regulatory system, ATP-binding cassette transporters, and bacterial secretion system. The upregulation of these metabolic pathways also contributed to the dissemination of ARGs.

Metagenomics reveals the potential transmission risk of resistomes from urban park environment to human

Urban parks play a significant role in urban ecosystems and are strongly associated with human health. Nevertheless, the biological contamination of urban parks - opportunistic pathogens and antibiotic resistance genes (ARGs) - has been poorly reported. Here, metagenomic and 16 S rRNA sequencing methods were used to study the distribution and assembly of opportunistic pathogens and ARGs in soil and water from nine parks in Lanzhou city, and further compared them with local human gut microbiomes to investigate the potential transmission risk. Our results revealed that the most important type of drug resistance in urban parks was multidrug resistance, with various resistance mechanisms. Approximately half of ARGs were shared between human gut and park environment, and it was noteworthy that cross-species transmission might exist among some high-risk ARGs, such as mepA and mdtE, with a significant enrichment in human gut. Metagenomic binning uncovered several bacterial genomes carrying adjacent ARGs, MGEs, and virulence genes, indicating a possibility that these genes may jointly transfer among different environments, particularly from park environment to human. Our results provided a reference point for the management of environmental pollutants in urban parks.

Disinfectant polyhexamethylene guanidine triggered simultaneous efflux pump antibiotic- and metal-resistance genes propagation during sludge anaerobic digestion

The environmental transmission of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) exerted devastating threats to global public health, and their interactions with other emerging contaminants (ECs) have raised increasing concern. This study investigated that the abundances of ARGs and MRGs with the predominant type of efflux pump were simultaneously increased (8.4-59.1%) by disinfectant polyhexamethylene guanidine (PHMG) during waste activated sludge (WAS) anaerobic digestion. The aggregation of the same microorganisms (i.e., Hymenobacter and Comamonas) and different host bacteria (i.e., Azoarcus and Thauera) were occurred upon exposure to PHMG, thereby increasing the co-selection and propagation of MRGs and ARGs by vertical gene transfer. Moreover, PHMG enhanced the process of horizontal gene transfer (HGT), facilitating their co-transmission by the same mobile genetic elements (20.2-223.7%). Additionally, PHMG up-regulated the expression of critical genes (i.e., glnB, trpG and gspM) associated with the HGT of ARGs and MRGs (i.e., two-component regulatory system and quorum sensing) and exocytosis system (i.e., bacterial secretion system). Structural equation model analysis further verified that the key driver for the simultaneous enrichment of ARGs and MRGs under PHMG stress was microbial community structure. The study gives new insights into the aggravated environmental risks and mechanisms of ECs in sludge digestion system, providing guidance for subsequent regulation and control of ECs.

Deciphering the adaptation mechanism of anammox consortia under sulfamethoxazole stress: A model coupling resistance accumulation and interspecies-cooperation

Sulfamethoxazole (SMX) is frequently detected in wastewater where anammox applications are promising. While it has been demonstrated that anammox consortia can adapt to SMX stress, the underlying community adaptation strategy has not yet been fully addressed. Therefore, in this study, we initially ascertained anammox consortia's ability to co-metabolize SMX in batch tests. Then, a 200-day domestication process of anammox consortia under SMX stress was carried out with community variations and transcriptional activities monitored by metagenomic and metatranscriptomic sequencing techniques. Despite the initial drop to 41.88 %, the nitrogen removal efficiency of the anammox consortia rebounded to 84.64 % post-domestication under 5 mg/L SMX. Meanwhile, a 4.85-fold accumulation of antibiotic resistance genes (ARGs) under SMX stress was observed as compared to the control group. Interestingly, the anammox consortia may unlock the SMX-inhibited folate synthesis pathway through a novel interspecies cooperation triangle among Nitrospira (NAA), Desulfobacillus denitrificans (DSS1), and the core anammox population Candidatus Brocadia sinica (AMX1), in which the modified dihydropteroate synthase (encoded by sul1) of NAA reconnected the symbiotic cooperation between AMX1 and DSS1. Overall, this study provides a new model for the adaptation strategies of anammox consortia to SMX stress.

Deciphering the impact of organic loading rate and digestate recirculation on the occurrence patterns of antibiotics and antibiotic resistance genes in dry anaerobic digestion of kitchen waste

Organic loading rate (OLR) is crucial for determining the stability of dry anaerobic digestion (AD). Digestate recirculation contributes to reactor stability and enhances methane production. Nevertheless, the understanding of how OLR and digestate recirculation affect the abundance and diversity of antibiotics and antibiotic resistance genes (ARGs), as well as the mechanisms involved in the dissemination of ARGs, remains limited. This study thoroughly investigated this critical issue through a long-term pilot-scale experiment. The metabolome analyses revealed the enrichment of various antibiotics, such as aminoglycoside, tetracycline, and macrolide, under low OLR conditions (OLR ≤ 4.0 g·VS/L·d) and the reactor instability. Antibiotics abundance decreased by approximately 19.66-31.69 % during high OLR operation (OLR ≥ 6.0 g·VS/L·d) with digestate recirculation. The metagenome analyses demonstrated that although low OLR promoted reactor stability, it facilitated the proliferation of antibiotic-resistant bacteria, such as Pseudomonas, and triggered functional profiles related to ATP generation, oxidative stress response, EPS secretion, and cell membrane permeability, thereby facilitating horizontal gene transfer (HGT) of ARGs. However, under stable operation at an OLR of 6.0 g·VS/L·d, there was a decrease in ARGs abundance but a notable increase in human pathogenic bacteria (HPB) and mobile genetic elements (MGEs). Subsequently, during reactor instability, the abundance of ARGs and HPB increased. Notably, during digestate recirculation at OLR levels of 6.0 and 7.0 g·VS/L·d, the process attenuated the risk of ARGs spread by reducing the diversity of ARGs hosts, minimizing interactions among ARGs hosts, ARGs, and MGEs, and weakening functional profiles associated with HGT of ARGs. Overall, digestate recirculation aids in reducing the abundance of antibiotics and ARGs under high OLR conditions. These findings provide advanced insights into how OLR and digestate recirculation affect the occurrence patterns of antibiotics and ARGs in dry AD.

Dissecting the ecological risks of sulfadiazine degradation intermediates under different advanced oxidation systems: From toxicity to the fate of antibiotic resistance genes

The incomplete degradation of antibiotics in water can produce intermediates that carry environmental risks and thus warrant concerns. In this study, the degradation of high concentrations of antibiotic sulfadiazine (SDZ) by advanced oxidation processes that leverage different reactive oxide species was systematically evaluated in terms of the influence of different degradation intermediates on the propagation of antibiotic resistance genes (ARGs). The ozone, persulfate, and photocatalytic oxidation systems for SDZ degradation are dominated by ozone, direct electron transfer, and singlet oxygen, hole, and superoxide radicals, respectively. These processes produce 15 intermediates via six degradation pathways. Notably, it was determined that three specific intermediates produced by the ozone and persulfate systems were more toxic than SDZ. In contrast, the photocatalytic system did not produce any intermediates with toxicity exceeding that of SDZ. Microcosm experiments combined with metagenomics confirmed significant changes in microbiota community structure after treatment with SDZ and its intermediates, including significant changes in the abundance of Flavobacterium, Dungenella, Archangium, and Comamonas. This treatment also led to the emergence of sulfonamide ARGs. The total abundance of sulfonamide ARGs was found to be positively correlated with residual SDZ concentration, with the lowest total abundance observed in the photocatalytic system. Additionally, the correlation analysis unveiled microbiota carrying sulfonamide ARGs.

Neglected risks of enhanced antimicrobial resistance and pathogenicity in anaerobic digestion during transition from thermophilic to mesophilic

Minimization of antibiotic resistance genes (ARGs) and potential pathogenic antibiotic-resistant bacteria (PARB) during anaerobic digestion (AD) is significantly impacted by temperature. However, knowledge on how ARGs and PARB respond to temperature transition from thermophilic to mesophilic is limited. Here, we combined metagenomic-based with culture-based approaches and revealed the risks of antimicrobial resistance and pathogenicity during transition from 55 °C to 35 °C for AD, with strategies of sharp (ST, one-step by 20 °C/d) and mild (MT, step-wise by 1 °C/d). Results indicated a lower decrease in methane production with MT (by 38.9%) than ST (by 88.8%). Phenotypic assays characterized a significant propagation of multi-resistant lactose-fermenting Enterobacteriaceae and indicator pathogens after both transitions, especially via ST. Further genomic evidence indicated a significant increase of ARGs (29.4-fold), virulence factor genes (1.8-fold) and PARB (65.3-fold) after ST, while slight enrichment via MT. Bacterial succession and enhanced horizontal transfer mediated by mobile genetic elements promoted ARG propagation in AD during transition, which was synchronously exacerbated through horizontal transfer mechanisms mediated by cellular physiological responses (oxidative stress, membrane permeability, bacterial conjugation and transformation) and co-selection mechanisms of biomethanation metabolic functions (acidogenesis and acetogenesis). This study reveals temperature-dependent resistome and pathogenicity development in AD, facilitating microbial risk control.

Leaching of antibiotic resistance genes and microbial assemblages following poultry litter applications in karst and non-karst landscapes

Antibiotic resistance is increasingly recognized as a critical challenge affecting human, animal, and environmental health. Yet, environmental dynamics and transport of antibiotic resistance genes (ARGs) and microbial communities in karst and non-karst leachate following poultry litter land applications are not well understood. This study investigates impacts of broiler poultry litter application on the proliferation of ARGs (tetW, qnrS, ermB, sulI, and blaCTX-M-32), class 1 integron (intI1 i), and alterations in microbial communities (16S rRNA) within karst derived soils, which are crucial and under-researched systems in the global hydrological cycle, and non-karst landscapes. Using large, intact soil columns (45 cm diam. × 100 cm depth) from karst and non-karst landscapes, the role of preferential flow and ARG transport in leachate was enumerated following surface application of poultry litter and simulated rain events. This research demonstrated that in poultry litter amended karst soils, ARG (i.e., ermB and tetW) abundance in leachate increased 1.5 times compared to non-karst systems (p < 0.05), highlighting the influence of geological factors on ARG proliferation. Notably, microbial communities in karst soil leachate exhibited increased diversity and abundance, suggesting a potential linkage between microbial composition and ARG presence. Further, our correlation and network analyses identified relationships between leachate ARGs, microbial taxa, and physicochemical properties, underscoring the complex interplay in these environmentally sensitive areas. These findings illuminate the critical role of karst systems in shaping ARG abundance and pollutant dispersal and microbial community dynamics, thus emphasizing the need for landscape-specific approaches in managing ARG dissemination to the environment. This study provides a deeper understanding of hydrogeological ARG dynamics but also lays the groundwork for future research and strategies to mitigate ARG dissemination through targeted manure applications across agricultural landscapes.

Accelerated dissemination of antibiotic resistant genes via conjugative transfer driven by deficient denitrification in biochar-based biofiltration systems

Biofiltration systems harbored and disseminated antibiotic resistance genes (ARGs), when confronting antibiotic-contained wastewater. Biochar, a widely used environmental remediation material, can mitigate antibiotic stress on adjoining microbes by lowering the availability of sorbed antibiotics, and enhance the attachment of denitrifiers. Herein, bench-scale biofiltration systems, packed with commercial biochars, were established to explore the pivotal drivers affecting ARG emergence. Results showed that biofiltration columns, achieving higher TN removal and denitrification capacity, showed a significant decrease in ARG accumulation (p < 0.05). The relative abundance of ARGs (0.014 ± 0.0008) in the attached biofilms decreased to 1/5-folds of that in the control group (0.065 ± 0.004). Functional analysis indicated ARGs' accumulation was less attributed to ARG activation or horizontal gene transfer (HGT) driven by sorbed antibiotics. Most denitrifiers, like Bradyrhizobium, Geothrix, etc., were found to be enriched and host ARGs. Nitrosative stress from deficient denitrification was demonstrated to be the dominant driver for affecting ARG accumulation and dissemination. Metagenomic and metaproteomic analysis revealed that nitrosative stress promoted the conjugative HGT of ARGs mainly via increasing the transmembrane permeability and enhancing the amino acid transport and metabolism, such as cysteine, methionine, and valine metabolism. Overall, this study highlighted the risks of deficient denitrification in promoting ARG transfer and transmission in biofiltration systems and natural ecosystems.

Deciphering the reduction of antibiotic resistance genes (ARGs) during medium-chain fatty acids production from waste activated sludge: Driven by inhibition of ARGs transmission and shift of microbial community

Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) by chain extension (CE) is a promising technology. However, the effects and mechanisms of CE process on the fate of antibiotic resistance genes (ARGs) remain unclear. In this study, the results showed that the removal efficiency of ARGs was 81.15 % in CE process, suggesting its efficacy in reducing environmental risks. Further, the observed decrease in mobile genetic elements (MGEs) indicated that CE process restricted the horizontal gene transfer (HGT). Complementing this, the increase in soluble organic matters and extracellular 16 S rDNA confirmed that MCFAs production caused bacterial damage. Decreased intracellular ARGs and increased extracellular ARGs further revealed that MCFAs production impaired ARGs hosts, thereby limiting the vertical gene transfer (VGT) of ARGs. Shift of microbial community combined with co-occurrence network analysis demonstrated that functional bacteria without host potential for ARGs were enriched, but potential ARGs and MGEs hosts decreased, showing the role of functional bacterial phylogeny and selection pressure of MCFAs in reducing ARGs. Finally, partial least squares path model was used to systematic verify the mechanism of ARGs removal in CE process, which was attributed to the inhibition of ARGs transmission (HGT and VGT) and shift of microbial community.

The combination of ciprofloxacin and dialkyldimethyl ammonium compound synergistically proliferated intracellular resistance genes in nitrifying system

Antibiotics and quaternary ammonium compounds (QACs) usually co-exist in wastewater treatment plants. Hence, three sequencing batch reactors were established and named as R1, R2 and R3, to investigate the effects of individual and combined exposure of different concentrations of ciprofloxacin (CIP) (0.2, 1.0 and 2.0 mg/L) and dialkyldimethyl ammonium compound (DADMAC) (0.4, 2.0 and 4.0 mg/L) on the performance, microbial community structures and resistance genes (RGs) in nitrifying system during 150 days. Results showed that CIP had a slight effect on ammonia oxidation activity, while 2.0 and 4.0 mg/L DADAMAC could obviously inhibit it, and the combination of CIP and DADMAC had a synergistic inhibitory effect. Besides, both CIP and DADMAC caused partial nitrification, and the order of nitrite accumulation rate was ranked as R3 > R2 > R1. The combination of CIP and DADMAC had an antagonistic effect on the increase of sludge particle size and α-Helix/(β-Sheet + Random coil) was lowest in R3 (0.40). The combination of CIP and DADMAC synergistically stimulated most intracellular RGs in sludge, and the relative abundances of target RGs (e.g., qacEdelta1-01, qacH-01 and qnrS) at the end of operation in R3 were increased by 4.61-18.19 folds compared with those in CK, which were 1.34-5.57 folds higher than the R1 and R2. Moreover, the combination of CIP and DADMAC also promoted the transfer of RGs from sludge to water and enriched more potential hosts of RGs, further promoting the spread of RGs in nitrifying system. Thus, the combined pollution of CIP and DADMAC in wastewaters should attract more attentions.

Unraveling the nexus: Microplastics, antibiotics, and ARGs interactions, threats and control in aquaculture - A review

In recent years, aquaculture has expanded rapidly to address food scarcity and provides high-quality aquatic products. However, this growth has led to the release of significant effluents, containing emerging contaminants like antibiotics, microplastics (MPs), and antibiotic resistance genes (ARGs). This study investigated the occurrence and interactions of these pollutants in aquaculture environment. Combined pollutants, such as MPs and coexisting adsorbents, were widespread and could include antibiotics, heavy metals, resistance genes, and pathogens. Elevated levels of chemical pollutants on MPs could lead to the emergence of resistance genes under selective pressure, facilitated by bacterial communities and horizontal gene transfer (HGT). MPs acted as vectors, transferring pollutants into the food web. Various technologies, including membrane technology, coagulation, and advanced oxidation, have been trialed for pollutants removal, each with its benefits and drawbacks. Future research should focus on ecologically friendly treatment technologies for emerging contaminants in aquaculture wastewater. This review provided insights into understanding and addressing newly developing toxins, aiming to develop integrated systems for effective aquaculture wastewater treatment.

The resistance change and stress response mechanisms of chlorine-resistant bacteria under microplastic stress in drinking water distribution system

The presence of both chlorine-resistant bacteria (CRB) and microplastics (MPs) in drinking water distribution systems (DWDS) poses a threat to water quality and human health. However, the risk of CRB bio evolution under the stress of MPs remains unclear. In this study, polypropylene (PP) and polyethylene (PE) were selected to study the adsorption and desorption behavior of sulfamethoxazole (SMX), and it was clear that MPs had the risk of carrying pollutants into DWDS and releasing them. The results of the antibiotic susceptibility test and disinfection experiment confirmed that MPs could enhance the resistance of CRB to antibiotics and disinfectants. Bacteria epigenetic resistance mechanisms were approached from multiple perspectives, including physiological and biochemical characteristics, as well as molecular regulatory networks. When MPs enter DWDS, CRB could attach to the surface of MPs and directly interact with both MPs and the antibiotics they release. This attachment process promoted changes in the composition and content of extracellular polymers (EPS) within cells, enhanced surface hydrophobicity, stimulated oxidative stress function, and notably elevated the relative abundance of certain antibiotic resistance genes (ARGs). This study elucidates the mechanism by which MPs alter the intrinsic properties of CRB, providing valuable insights into the effective avoidance of biological risks to water quality during CRB evolution.

Impacts of microplastic type on the fate of antibiotic resistance genes and horizontal gene transfer mechanism during anaerobic digestion

Microplastics (MPs) and antibiotic resistance genes (ARGs) are important pollutants in waste activated sludge (WAS), but their interactions during anaerobic digestion (AD) still need to be further explored. This study investigated variations in ARGs, mobile genetic elements (MGEs), and host bacteria during AD under the pressure of polyamide (PA), polyethylene (PE), and polypropylene (PP). The results showed that the MPs increased methane production by 11.7-35.5%, and decreased ARG abundance by 5.6-24.6%. Correlation analysis showed that the decrease of MGEs (plasmid, prophage, etc.) promoted the decrease of the abundance of multidrug, aminoglycoside and tetracycline resistance genes. Metagenomic annotation revealed that the reduction of key host bacteria (Arenimonas, Lautropia, etc.) reduced the abundance of major ARGs (rsmA, rpoB2, etc.). Moreover, PP MPs contributed to a reduction in the abundance of functional genes related to the production of reactive oxygen species, ATP synthesis, and cell membrane permeability, which was conducive to reducing the potential for horizontal gene transfer of ARGs. These findings provide insights into the treatment of organic waste containing MPs.

Microecology of aerobic denitrification system construction driven by cyclic stress of sulfamethoxazole

The construction of aerobic denitrification (AD) systems in an antibiotic-stressed environment is a serious challenge. This study investigated strategy of cyclic stress with concentration gradient (5-30 mg/L) of sulfamethoxazole (SMX) in a sequencing batch reactor (SBR), to achieve operation of AD. Total nitrogen removal efficiency of system increased from about 10 % to 95 %. Original response of abundant-rare genera to antibiotics was changed by SMX stress, particularly conditionally rare or abundant taxa (CRAT). AD process depends on synergistic effect of heterotrophic nitrifying aerobic denitrification bacteria (Paracoccus, Thauera, Hypomicrobium, etc). AmoABC, napA, and nirK were functionally co-expressed with multiple antibiotic resistance genes (ARGs) (acrR, ereAB, and mdtO), facilitating AD process. ARGs and TCA cycling synergistically enhance the antioxidant and electron transport capacities of AD process. Antibiotic efflux pump mechanism played an important role in operation of AD. The study provides strong support for regulating activated sludge to achieve in situ AD function.

Fe-Mn binary oxides improve the methanogenic performance and reduce the environmental health risks associated with antibiotic resistance genes during anaerobic digestion

Increasing evidence indicates that metal oxides can improve the methanogenic performance during anaerobic digestion (AD) of piggery wastewater. However, the impacts of composite metal oxides on the methanogenic performance and risk of antibiotic resistance gene (ARG) transmission during AD are not fully understood. In this study, different concentrations of Fe-Mn binary oxides (FMBO at 0, 250, 500, and 1000 mg/L) were added to AD to explore the effects of FMBO on the process. The methane yield was 7825.1 mL under FMBO at 250 mg/L, 35.2% higher than that with FMBO at 0 mg/L. PICRUSt2 functional predictions showed that FMBO promoted the oxidation of acetate and propionate, and the production of methane from the substrate, as well as increasing the abundances of most methanogens and genes encoding related enzymes. Furthermore, under FMBO at 250 mg/L, the relative abundances of 14 ARGs (excluding tetC and sul2) and four mobile gene elements (MGEs) decreased by 24.7% and 55.8%, respectively. Most of the changes in the abundances of ARGs were explained by microorganisms, especially Bacteroidetes (51.20%), followed by MGEs (11.98%). Thus, the methanogenic performance of AD improved and the risk of horizontal ARG transfer decreased with FMBO, especially at 250 mg/L.

Ofloxacin weakened treatment performance of rural domestic sewage in an aerobic biofilm system by affecting biofilm resistance, bacterial community, and functional genes

Ofloxacin (OFL) is a typical fluoroquinolone antibiotic widely detected in rural domestic sewage, however, its effects on the performance of aerobic biofilm systems during sewage treatment process remain poorly understood. We carried out an aerobic biofilm experiment to explore how the OFL with different concentrations affects the pollutant removal efficiency of rural domestic sewage. Results demonstrated that the OFL negatively affected pollutant removal in aerobic biofilm systems. High OFL levels resulted in a decrease in removal efficiency: 9.33% for chemical oxygen demand (COD), 18.57% for ammonium (NH4+-N), and 8.49% for total phosphorus (TP) after 35 days. The findings related to the chemical and biological properties of the biofilm revealed that the OFL exposure triggered oxidative stress and SOS responses, decreased the live cell number and extracellular polymeric substance content of biofilm, and altered bacterial community composition. More specifically, the relative abundance of key genera linked to COD (e.g., Rhodobacter), NH4+-N (e.g., Nitrosomonas), and TP (e.g., Dechlorimonas) removal was decreased. Such the OFL-induced decrease of these genera might result in the down-regulation of carbon degradation (amyA), ammonia oxidation (hao), and phosphorus adsorption (ppx) functional genes. The conventional pollutants (COD, NH4+-N, and TP) removal was directly affected by biofilm resistance, functional genes, and bacterial community under OFL exposure, and the bacterial community played a more dominant role based on partial least-squares path model analysis. These findings will provide valuable insights into understanding how antibiotics impact the performance of aerobic biofilm systems during rural domestic sewage treatment.

Oxygen mediated mobilization and co-occurrence of antibiotic resistance in lab-scale bioreactor using metagenomic binning

Sub-lethal levels of antibiotic stimulate bacteria to generate reactive oxygen species (ROS) that promotes emergence and spread of antibiotic resistance mediated by mobile genetic elements (MGEs). Nevertheless, the influence of dissolved oxygen (DO) levels on mobility of antibiotic resistance genes (ARGs) in response to ROS-induced stress remains elusive. Thus, the study employs metagenomic assembly and binning approaches to decipher mobility potential and co-occurrence frequency of ARGs and MGEs under hyperoxic (5.5-7 mgL- 1), normoxic (2.5-4 mgL- 1), and hypoxic (0.5-1 mgL- 1) conditions in lab-scale bioreactor for 6 months. Among 163 high-quality metagenome-assembled genomes (MAGs) recovered from 13 metagenomes, 42 MAGs harboured multiple ARGs and were assigned to priority pathogen group. Total ARG count increased by 4.3 and 2.5% in hyperoxic and normoxic, but decreased by 0.53% in hypoxic conditions after 150 days. On contrary, MGE count increased by 7.3-1.3% in all the DO levels, with only two ARGs showed positive correlation with MGEs in hypoxic compared to 20 ARGs under hyperoxic conditions. Opportunistic pathogens (Escherichia, Klebsiella, Clostridium, and Proteus) were detected as potential hosts of ARGs wherein co-localisation of critical ARG gene cassette (sul1, dfr1,adeF, and qacC) were identified in class 1 integron/Tn1 family transposons. Thus, enhanced co-occurrence frequency of ARGs with MGEs in pathogens suggested promotion of ARGs mobility under oxidative stress. The study offers valuable insights into ARG dissemination and hosts dynamics that is essential for controlling oxygen-related stress for mitigating MGEs and ARGs in the environment.

Impact of uranium on antibiotic resistance in activated sludge

The emergence of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in the environment is well established as a human health crisis. The impact of radioactive heavy metals on ecosystems and ultimately on human health has become a global issue, especially for the regions suffering various nuclear activities or accidents. However, whether the radionuclides can affect the fate of antibiotic resistance in bacteria remains poorly understood. Here, the dynamics of ARB, three forms of ARGs-intracellular ARGs (iARGs), adsorbed extracellular ARGs (aeARGs), and free extracellular ARGs (feARGs)-and microbial communities were investigated following exposure to uranium (U), a representative radioactive heavy metal. The results showed that 90-d of U exposure at environmentally relevant concentrations of 0.05 mg/L or 5 mg/L significantly increased the ARB concentration in activated sludge (p < 0.05). Furthermore, 90-d of U exposure slightly elevated the absolute abundance of aeARGs (except tetO) and sulfonamide iARGs, but decreased tetracycline iARGs. Regarding feARGs, the abundance of tetC, tetO, and sul1 decreased after 90-d of U stress, whereas sul2 showed the opposite trend. Partial least-squares path model analysis revealed that the abundance of aeARGs and iARGs under U stress was predominantly driven by increased cell membrane permeability/intI1 abundance and cell membrane permeability/reactive oxygen species concentration, respectively. Conversely, the changes in feARGs abundance depended on the composition of the microbial community and the expression of efflux pumps. Our findings shed light on the variations of ARGs and ARB in activated sludge under U exposure, providing a more comprehensive understanding of antibiotic resistance risks aggravated by radioactive heavy metal-containing wastewater.

Nanoscale zero-valent iron alleviate antibiotic resistance risk during managed aquifer recharge (MAR) by regulating denitrifying bacterial network

The frequent occurrence of antibiotics in reclaimed water is concerning, in the case of managed aquifer recharge (MAR), it inevitably hinders further water purification and accelerates the evolutionary resistance in indigenous bacteria. In this study, we constructed two column reactors and nanoscale zero-valent iron (nZVI) amendment was applied for its effects on water quality variation, microbial community succession, and antibiotic resistance genes (ARGs) dissemination, deciphered the underlying mechanism of resistance risk reduction. Results showed that nZVI was oxidized to iron oxides in the sediment column, and total effluent iron concentration was within permissible limits. nZVI enhanced NO3--N removal by 15.5% through enriching denitrifying bacteria and genes, whereas made no effects on oxacillin (OXA) removal. In addition, nZVI exhibited a pivotal impact on ARGs and plasmids decreasing. Network analysis elucidated that the diversity and richness of ARG host declined with nZVI amendment. Denitrifying bacteria play a key role in suppressing horizontal gene transfer (HGT). The underlying mechanisms of inhibited HGT included the downregulated SOS response, the inhibited Type-Ⅳ secretion system and the weakened driving force. This study afforded vital insights into ARG spread control, providing a reference for future applications of nZVI in MAR.

Alternations of antibiotic resistance genes and microbial community dynamics on shared bicycles before and after pandemic lockdown

The prevalence of shared bicycles has raised concerns over their potential to transmit pathogens and microbes harboring antibiotic resistance genes (ARGs), which pose significant human health risks. This study investigated the impact of anthropogenic activities on the composition of ARGs and microbial communities on shared bicycles during the COVID-19 pandemic and subsequent lockdown when shared bicycle usage was altered. A total of 600 swab samples from shared bicycle surfaces were collected in Shanghai before and during COVID-19 lockdown periods. Even during lockdown, 12 out of 14 initially detected ARG subtypes persisted, indicating their tenacity in the face of reduced anthropogenic activities. These ARGs displayed significantly higher absolute and relative abundance levels before the lockdown. In addition, the percentage of potential pathogens in the total microbial abundance remained at 0.029 % during the lockdown, which was lower than the pre-lockdown percentage of 0.035 % and suggested that these risks persist within shared bicycle systems. Interestingly, although microbial abundance decreased without the consecutive use of shared bicycles during lockdown, the microbial diversity increased under the impact of restricted anthropogenic activities (p < 0.001). This emphasizes the need for continuous monitoring and research to comprehend microbial community behaviors in various environments. This study uncovered the underlying impacts of the COVID-19 lockdown on the microbial and ARG communities of shared bicycles, providing comprehensive insights into the health management of shared transportation. Although lockdown can decrease the abundance of ARGs and potential pathogens, additional interventions are needed to prevent their continued spread.

Effects of oxytetracycline on variation in intracellular and extracellular antibiotic resistance genes during swine manure composting

This research aimed to investigate the alterations in extracellular (eARGs) and intracellular (iARGs) antibiotic resistance genes in response to oxytetracycline (OTC), and unravel the dissemination mechanism of ARGs during composting. The findings revealed both low (L-OTC) and high contents (H-OTC) of OTC significantly enhanced absolute abundance (AA) of iARGs (p < 0.05), compared to CK (no OTC). Composting proved to be a proficient strategy for removing eARGs, while AA of eARGs was significantly enhanced in H-OTC (p < 0.05). OTC resulted in an increase in AA of mobile genetic elements (MGEs), ATP levels, antioxidant and DNA repair enzymes in bacteria in compost product. Structural equation model further demonstrated that OTC promoted bacterial DNA repair and antioxidant enzyme activities, altered bacterial community and enhanced MGEs abundance, thereby facilitating iARGs dissemination. This study highlights OTC can increase eARGs and iARGs abundance, underscoring the need for appropriate countermeasures to mitigate potential hazards.

Insights into the roles of biochar pores toward alleviating antibiotic resistance genes accumulation in biofiltration systems

Biofiltration systems would harbor and spread various antibiotic resistance genes (ARGs) when treating antibiotic micro-pollution, constituting a potential ecological risk. This study aimed to investigate the effects of biochar pores on ARG emergence and related microbial response mechanisms in bench-scale biofiltration systems. Results showed that biochar pores effectively reduced the absolute copies of the corresponding ARGs sul1 and sul2 by 54.1% by lowering the sorbed-SMX's bioavailability compared to non-porous anthracite. An investigation of antimicrobial resistomes revealed a considerable decrease in the abundance and diversity of ARGs and mobile gene elements. Metagenomic and metaproteomic analysis demonstrated that biochar pores induced the changeover of microbial defense strategy against SMX from blocking SMX uptake by EPS absorbing to SMX biotransformation. Microbial SOS response, antibiotic efflux pump, EPS secretion, and biofilm formation were decreased. Functions related to SMX biotransformation, such as sadABC-mediated transformation, xenobiotics degradation, and metabolism, were significantly promoted.

Carbamazepine facilitated horizontal transfer of antibiotic resistance genes by enhancing microbial communication and aggregation

Antimicrobial resistance is a global health security issue of widespread concern. Recent studies have unveiled the potential contribution of non-antibiotics to the emergence of antimicrobial resistance. This study investigated the effect of carbamazepine, a non-antibiotic pharmaceutical, on the fate of antibiotic resistance genes (ARGs) during anaerobic digestion. The results, as revealed by both metagenomic sequencing and absolute quantification, demonstrated that carbamazepine induced the enrichment of ARGs and increased the abundance of ARGs hosts by 1.2-2.1 times. Carbamazepine facilitated microbial aggregation and intercellular communication by upregulating functional genes associated with two-component systems, quorum sensing and type IV secretion systems, thereby increasing the frequency of ARGs conjugation. Furthermore, carbamazepine induced the acquisition of ARGs by pathogens and elevated the overall pathogenic abundance. This study revealed the mechanisms of microbial self-regulation and ARGs transmission under carbamazepine stress, highlighting the potential health risks posed by non-antibiotic pharmaceuticals during the safe disposal of sludge.

Response behavior of antibiotic resistance genes and human pathogens to slope gradient and position: An environmental risk analysis in sloping cultivated land

Soils, especially in farmlands, are key media for the transmission of antibiotic resistance genes (ARGs) and their hosts from the environment to humans. Sloping farmland is an important agricultural resource, but there lack of studies on the fate and risk of ARGs in sloping land. Also, the behavior and drivers of ARGs in response to slope gradient and position are unclear. Here, metagenomics was used to investigate the profiles of ARGs, mobile genetic elements, and microbial communities in soils from lands of five slope gradients (5°, 10°, 15°, 20°, and 25°) with two slope positions (uphill and downhill). Results showed that while the abundance (except 15°) and diversity (except 20°) of ARGs increased as the slope gradient increased, the diversity of ARGs with health risk, especially the high-risk ones, decreased. For slope positions, abundant and diverse ARGs were more likely to accumulate at downhill. Furthermore, 52 bacterial genera and 12 human pathogenic bacteria (HPB) species were identified as the potential hosts for ARGs with high risk, and abundant HPB species were also detected in the soils with low gradients at downhill. Moreover, the structural equation model analysis revealed that the slope gradient and the slope position have both direct and indirect effects on the abundance of ARGs. Further correlation analysis revealed that the slope gradient has a positive effect (p < 0.05) on nitrite nitrogen in the soils. Also, the slope position has a negative effect (p < 0.05) on total phosphorus and microbial nitrogen, while positively affected (p < 0.05) on particulate nitrogen and microbial carbon, which were the key factors driving the behavior of ARGs. Overall, this study provided comprehensive information on ARGs with health risks and their potential pathogenic hosts in sloping farmland. It can be important for controlling antibiotic resistance transmission and be consistent with the One Health framework.

Responses of antibiotic resistance genes in the enhanced biological phosphorus removal system under various antibiotics: Mechanisms and implications

The effects of antibiotics on the proliferation of antibiotic resistant genes (ARGs) in WWTPs have drawn great attention in recent years. The effects of antibiotics on ARGs in the enhanced biological phosphorus removal (EBPR) system and its mechanisms, however, are still not well understood. In this study, EBPR systems were constructed using activated sludge to investigate the effects of ten commonly detected antibiotics in the environment on the proliferation of ARGs and the mechanisms involved. The results showed that the total abundance of ARGs increased to varying degrees with the addition of different antibiotics (0.05 mmol/L), and the top 30 ARGs increased by 271.1 % to 370.0 %. Mobile genetic elements (MGEs), functional modules, and the bacteria community were consistently related to the changes in ARGs. Refractory antibiotics, in particular, have a stronger promoting effect on transduction in the EBPR system. The insertion sequence common region (ISCR) and transposon (Tnp) were identified as crucial factors in the proliferation of ARGs. Moreover, the risk of polyphosphate accumulating organisms (PAOs) carrying ARGs in the presence of antibiotics should not be ignored. Our findings emphasize the potential efficacy of employing strategies that target the reduction of MGEs, regulation of cellular communication, and management of microbial communities to effectively mitigate the risks associated with ARGs.

Antibiotics resistance removal from piggery wastewater by an integrated anaerobic-aerobic biofilm reactor: Efficiency and mechanism

Antibiotic resistance residual in piggery wastewater poses serious threat to environment and human health. Biological treatment process is commonly installed to remove nutrient from piggery wastewater and also effective in removing antibiotics to varying degrees. But the specific pathways and mechanisms involved in the removal of antibiotic resistance are not yet well-understood. An integrated anaerobic-aerobic biofilm reactor (IAOBR) has been demonstrated efficient in removing conventional nutrients. It is here shown that the IAOBR effectively removed 79.0% of Sulfonamides, 55.7% of Tetracyclines and 53.6% of Quinones. Antibiotic resistance bacteria (ARB) were simultaneously inactivated by ~0.5 logs. Antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were decreased by 0.51 logs and 0.42 logs, respectively. The antibiotics were mainly removed through aerobic compartments of the IAOBR. The mass loss of antibiotics in the reactor was achieved by biodegradation and adsorption, accounting for 52.1% and 47.9%, respectively. An obvious accumulation of ARGs was observed in the activated sludge. The potential host of ARGs was analyzed via microbial community and network. Partial least squares-structural equation model and correlation analysis revealed that the enrichment of ARGs was positively affected by MGEs, followed by bacterial community and ARBs, but the effect of antibiotics on ARGs was negative. Outcomes of this study provide valuable insights into the mechanisms of antibiotic resistance removal in biological treatment processes.

Disinfectant sodium dichloroisocyanurate synergistically strengthened sludge acidogenic process and pathogens inactivation: Targeted upregulation of functional microorganisms and metabolic traits via self-adaptation

Harmless and resourceful treatment of waste activated sludge (WAS) have been the crucial goal for building environmental-friendly and sustainable society, while the synergistic realization approach is currently limited. This work skillfully utilized the disinfectant sodium dichloroisocyanurate (NaDCC) to simultaneously achieve the pathogenic potential inactivation (decreased by 60.1 %) and efficient volatile fatty acids (VFAs) recovery (increased by 221.9 %) during WAS anaerobic fermentation in rather cost-effective way (Chemicals costs:0.4 USD/kg VFAs versus products benefits: 2.68 USD/kg chemical). Mechanistic analysis revealed that the C=O and NCl bonds in NaDCC could spontaneously absorb sludge (binding energy -4.9 kJ/mol), and then caused the sludge disintegration and organic substrates release for microbial utilization due to the oxidizability of NaDCC. The disruption of sludge structure along with the increase of bioavailable fermentation substrates contributed to the selectively regulation of microbial community via enriching VFAs-forming microorganisms (e.g., Pseudomonas and Streptomyces) and reducing VFAs-consuming microorganisms, especially aceticlastic methanogens (e.g., Methanothrix and Methanospirillum). Correspondingly, the metabolic functions of membrane transport, substrate metabolism, pyruvate metabolism, and fatty acid biosynthesis locating in the central pathway of VFAs production were all upregulated while the methanogenic step was inhibited (especially acetate-type methanogenic pathway). Further exploration unveiled that for those enriched functional anaerobes were capable to activate the self-adaptive systems of DNA replication, SOS response, oxidative stress defense, efflux pump, and energy metabolism to counteract the unfavorable NaDCC stress and maintain high microbial activities for efficient VFAs yields. This study would provide a novel strategy for synergistic realization of harmless and resourceful treatment of WAS, and identify the interrelations between microbial metabolic regulations and adaptive responses.

Insights into antibiotic resistance-related changes in microbial communities, resistome and mobilome in paddy irrigated with reclaimed wastewater

Reclaimed wastewater (reclaimed wastewater, RWW) from municipal wastewater treatment plants for paddy irrigation is a well-established practice to alleviate water scarcity. However, the reuse may result in the persistent exposure of the paddy to residual antibiotics in RWW. Continuous presence of even low-level antibiotics can exert selective pressure on microbiota, resulting in the proliferation and dissemination of antibiotic resistance genes (ARGs) in paddy. In this study, metagenomic analysis was applied to firstly deciphered the effects of residual antibiotics on microbiome and resistome in constructed mesocosm-scale paddy soils. The diversity and abundance of ARG have remarkably risen with the increasing antibiotic concentration in RWW. Network analysis revealed that 28 genera belonging to six phyla were considered as the potential ARG hosts, and their abundances were enhanced with increasing antibiotic concentrations. A partial least-squares path model indicated that the microbial community was the principal direct driver of the ARG abundance and the resistome alteration in paddy soil under long-term RWW irrigation. Microbes may acquire ARGs via horizontal gene transfer. IntI1 could play an essential role in the propagation and spread of ARGs. Functional analysis suggested that enhanced SOS response and T4SSs (Type IV secretion systems) modules could stimulate horizontal transfer potential and promote the ARG abundance. The obtained results provide a scientific decision for assessing the ecological risk of RWW application.

Differential airway resistome and its correlations with clinical characteristics in Haemophilus- or Pseudomonas-predominant microbial subtypes of bronchiectasis

The prevalence and clinical correlates of antibiotic resistance genes (ARGs) in bronchiectasis are not entirely clear. We aimed to profile the ARGs in sputum from adults with bronchiectasis, and explore the association with airway microbiome and disease severity and subtypes. In this longitudinal study, we prospectively collected 118 sputum samples from stable and exacerbation visits of 82 bronchiectasis patients and 19 healthy subjects. We profiled ARGs with shotgun metagenomic sequencing, and linked these to sputum microbiome and clinical characteristics, followed by validation in an international cohort. We compared ARG profiles in bronchiectasis according to disease severity, blood and sputum inflammatory subtypes. Unsupervised clustering revealed a Pseudomonas predominant subgroup (n = 16), Haemophilus predominant subgroup (n = 48), and balanced microbiome subgroup (N = 54). ARGs of multi-drug resistance were over-dominant in the Pseudomonas-predominant subgroup, while ARGs of beta-lactam resistance were most abundant in the Haemophilus-predominant subgroup. Pseudomonas-predominant subgroup yielded the highest ARG diversity and total abundance, while Haemophilus-predominant subgroup and balanced microbiota subgroup were lowest in ARG diversity and total abundance. PBP-1A, ksgA and emrB (multidrug) were most significantly enriched in Haemophilus-predominant subtype. ARGs generally correlated positively with Bronchiectasis Severity Index, fluoroquinolone use, and modified Reiff score. 68.6% of the ARG-clinical correlations could be validated in an independent international cohort. In conclusion, ARGs are differentially associated with the dominant microbiome and clinical characteristics in bronchiectasis.

Prevalence of antibiotic resistance genes and virulence factors in the sediment of WWTP effluent-dominated rivers

In the context of increasing aridity due to climate changes, effluent from wastewater treatment plants (WWTPs) became dominant in some rivers. However, the prevalence of antibiotic resistance genes (ARGs) and virulence factors (VFs) in effluent-dominated rivers was rarely investigated. In this study, the profiles of ARGs and VFs in the sediment of two effluent-dominated rivers were revealed through the metagenomic sequencing technique. In each river, samples from the effluent discharge point (P site) and approximately 500 m downstream (D site) were collected. Results showed that the abundances of ARGs and VFs were both higher in D sites than those in P sites, indicating higher risks in the downstream areas. The compositions of ARGs were similar in the P sites of two rivers while being distinct in the D sites. The same was true for changes in the VFs compositions. Microbial community structure variations were the main driver for the changes in ARGs and VFs. Network analysis revealed that the interaction of ARGs and VF genes (VFGs) in sediment was intense. Two VFGs and eleven ARGs were identified to play important roles in the network. Metagenome-assembled genomes (MAGs) were generated to evaluate the coexistence of ARGs and VFGs at the single genome level. It was found that 38.4 % of the MAGs contained both ARGs and VFGs, and two MAGs were from pathogenic genera. These results suggested that high microbiological risks existed in effluent-dominated rivers, and necessary measures should be taken to prevent the potential threat to public health.

Comprehensive assessment of toxicity and environmental risk associated with sulfamethoxazole biodegradation in sulfur-mediated biological wastewater treatment

Incomplete mineralization of sulfamethoxazole (SMX) in wastewater treatment systems poses a threat to ecological health. The toxicity and environmental risk associated with SMX biodegradation in the sulfur-mediated biological process were examined for the first time through a long-term (180 days) bioreactor study and a series of bioassays. The results indicated that the sulfur-mediated biological system was highly resistant and tolerant to SMX toxicity, as evidenced by the enrichment of sulfate-reducing bacteria (SRB), the improved microbial metabolic activity, and the excellent performance on pollutants removal under long-term SMX exposure. SMX can be effectively biodegraded by the cleavage and rearrangement of the isoxazole ring, hydrogenation and hydroxylation reactions in sulfur-mediated biological wastewater system. These biodegradation pathways effectively reduced the acute toxicity, antibacterial activity, and ecotoxicities of SMX and its biotransformation products (TPs) in the effluent of the sulfur-mediated biological system. The TPs produced via hydrogenation (TP1), hydroxylation, and isoxazole ring cleavage (TP3, TP4, TP5, TP8, and TP9) exhibited lower toxicity than SMX. Under SMX stress, although the abundance of sulfonamide resistance genes increased, the total abundance of ARGs decreased due to the extrusion of some intracellular SMX by the efflux pump genes and the inactivation of some SMX through the biodegradation process. Efflux pump and inactivation, as the main resistance mechanisms of antibiotics in the sulfur-mediated biological system, play a crucial role in microbial self-defense. The findings of this study demonstrate the great potential of the sulfur-mediated biological system in SMX removal, detoxication, and ARGs environmental risk reduction.

Sanwei sandalwood decoction improves function of the gut microbiota in heart failure

Objective

To investigate the effects of Sanwei sandalwood decoction on improving function of the intestinal flora in doxorubicin-induced heart failure in rats.

Materials and methods

Thirty Sprague-Dawley rats were screened and randomly assigned into a blank group, a model group, and a Sanwei sandalwood decoction group (treatment group). The rat model of heart failure was prepared and established in the latter two groups. After successful model establishment, the treatment group received Sanwei sandalwood decoction by continuous gavage at 2 g/kg, once daily for 4 weeks. The other groups were given an equivalent volume of saline. After the final dose, fecal samples were collected from each group and analyzed by macrogenomics and nontargeted metabolomics to characterize the intestinal flora and associated metabolites.

Results

The composition of gut microbiota was significantly different between the three groups. There were 778,808 common genes between the blank and model groups, while 49,315 genes were lost and 521,008 were gained in the model group relative to the blank group. At the phylum level, all groups of rat fecal samples were dominated by Firmicutes, Bacteroidota, Actinobacteria, and Proteobacteria. At the genus level, the microbial community composition in all experimental groups of rat fecal samples was dominated by Lactobacillus, Bifidobacterium, Limosilactobacillus, Allobaculum, Prevotella, and Ligilactobacillus spp. Interestingly, cluster analysis was performed on the top 30 KEGG ontology (KO) terms displaying significant differences in relative abundance in the rat fecal microbiome among experimental groups. The relative frequency of posttranslational modification, coenzyme transport and metabolism, cell wall, membrane, and envelope biogenesis in the eggNOG and CAZy databases. In the nontargeted metabolomics, the group principal component analysis revealed that the groups were well distinguished from one another. The different metabolites were screened with VIP >1, and the KEGG different metabolite classification and enrichment analysis revealed that there includes 15 metabolites pathway, including loxoprofen, conifery-l-acetate, trichilin A, and others. The arachidonic acid pathway also accounted for a significant portion of the KEGG pathway classification analysis.

Conclusion

Sanwei sandalwood decoction positively affects the intestinal microbial environment of rats with heart failure, improving the gut dysbiosis that is caused by the condition. This treatment intervention inhibits the growth of pathogenic bacteria and promotes the growth of beneficial species.

Response of viable bacteria to antibiotics in aerobic granular sludge: Resistance mechanisms and behaviors, bacterial communities, and driving factors

The assessment of antimicrobial resistance (AMR) risk by DNA-based techniques mainly relies on total bacterial DNA. In this case, AMR risk recognition is restricted to the genotype level, lacking crucial phenotypic information, such as the distribution of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in dead and viable bacteria. This limitation hinders the recognition of AMR behavior. Herein, based on propidium monoazide (PMA) shielding method, this work firstly quantified the intracellular ARGs/MGEs in viable and dead bacteria, and the impact of viable bacteria composition on the formation of intracellular/extracellular polymeric substance-related /cell-free ARGs (i/e/cARGs) and MGEs (i/e/cMGEs) in aerobic granular sludge (AGS). The shielding efficiency of PMA against dead bacteria was optimized to be as high as 97.5% when the MLSS of AGS was 2.0 g/L. Under antibiotic stimulation, 29.0% ∼ 49.0% of iARGs/iMGEs were carried by viable bacteria, and the remaining proportion were carried by dead bacteria. 18 out of the top 20 dominant genera showed a change in abundance by more than 1% after PMA treatment. 29 viable hosts were identified to associate with 52 iARGs, of which 28 and 15 hosts were also linked to 40 eARGs and 26 cARGs. Also, partial least-squares path model and variance partitioning analysis disclosed that viable bacteria and i/e/cMGEs had a positive effect on i/e/cARGs, with both contributing as much as 64.5% to the total ARGs enrichment. These results better visualized the AMR risk carried by viable bacteria and the categories of viable hosts. This work provides a novel insight into analyzing the actual AMR risk and viable hosts, helping to the reduction and control of AMR in wastewater treatment plants.