Long-Term Impact of Field Applications of Sewage Sludge on Soil Antibiotic Resistome

Impact of different continuous fertilizations on the antibiotic resistome associated with a subtropical triple-cropping system over one decade

The prevalence of antibiotic resistance genes (ARGs) in agricultural soils has garnered significant attention. However, the long-term impacts of various nitroge (N)-substitution fertilization regimes on the distribution of soil ARGs and their dominant drivers in a subtropical triple-cropping system remain largely unexplored. This study employed a metagenomic approach to analyze soil ARGs, microbial communities, mobile genetic elements (MGEs), and viruses from a maize-maize-cabbage rotation field experiment with five different fertilization regimes. Soil samples were collected in 2012 and 2021. A total of 615 unique ARG subtypes were identified, with multidrug, bacitracin, and rifamycin resistance genes being the most abundant. Notably, ARG types. the continuous application of fresh chicken manure (CM) over 10 years significantly increased both the count of unique ARG subtypes and the total ARG abundance compared to other fertilization regimes, such as inorganic fertilizer and composted chicken manure. Specifically, the abundance of genes associated with antibiotic target replacement (e.g., sul1 and sul2) in the CM-treated soil rose by 8.83-fold from 2021 to 2012. Our random forest analysis revealed that the abundance of three MGEs (QacEdelta, plasmids, and IstB), two viral families (Myoviridae and Podoviridae), two bacterial phyla (Chloroflexi and Planctomycetes), and two environmental factors (pH and soil organic matter (SOM)) significantly influenced the distribution of ARGs. Furthermore, variance decomposition analysis underscored the critical roles of the three MGEs and the two viral families in the dissemination of ARGs, suggesting that horizontal gene transfer (HGT) may play a key role in ARG spread. These findings enhance our understanding of how different fertilization practices influence ARG dissemination in subtropical triple-cropping agroecosystems over the long term and provide valuable insights for optimizing fertilization management strategies.

Transmission and control strategies of antimicrobial resistance from the environment to the clinic: A holistic review

The environment serves as a significant reservoir of antimicrobial resistance (AMR) microbes and genes and is increasingly recognized as key source of clinical AMR. Modern human activities impose an additional burden on environmental AMR, promoting its transmission to clinical setting and posing a serious threat to human health and welfare. Therefore, a comprehensive review of AMR transmission from the environment to the clinic, along with proposed effective control strategies, is crucial. This review systematically summarized current research on the transmission of environmental AMR to clinical settings. Furthermore, the transmission pathways, horizontal gene transfer (HGT) mechanisms, as well as the influential drivers including triple planetary crisis that may facilitate AMR transfer from environmental species to clinical pathogens are highlighted. In response to the growing trend of AMR transmission, we propose insightful mitigation strategies under the One Health framework, integrating advanced surveillance and tracking technologies, interdisciplinary knowledge, multisectoral interventions, alongside multiple antimicrobial use and stewardship approaches to tacking development and spread of AMR.

Determinants of antimicrobial resistance in biosolids: A systematic review, database, and meta-analysis

Biosolids can provide a nutrient rich soil amendment, particularly for poor soils and semi-arid or drought-prone areas. However, there are concerns that sludge and biosolids could be a source of propagation and exposure to AMR determinants such as antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs). To inform risk assessment efforts, a systematic literature review was performed to build a comprehensive spreadsheet database of ARB and ARG concentrations in biosolids (and some sludges specified as intended for land application), along with 69 other quantitative and qualitative meta-data fields from 68 published studies describing sampling information and processing methods that can be used for modeling purposes. Mean ARG concentrations per gram in positive samples of biosolids ranged from -5.7 log10(gene copies [gc]/g) to 12.92 log10(gc/g) (with these range values reported per dry weight), and aqueous concentrations ranged from 0.9 log10(gc/L) to 14.6 log10(gc/L). Mean ARB concentrations per gram of biosolids ranged from 2.02 log10 (colony forming units [CFU]/g) to 9.00 log10 (CFU/g) (dry weight), and aqueous concentrations ranged from 3.23 log10 (CFU/L) to 12.0 log10 (CFU/L). ARG log removal values (LRVs) during sewage sludge stabilization were calculated from a meta-analysis of mean concentrations before and after stabilization from 31 studies, ranging from -2.05 to 5.52 logs. The classes of resistance most relevant for a risk assessment corresponded to sulfonamide (sul1 and sul2), tetracycline (tetZ, tetX, tetA and tetG), beta-lactam (blaTEM), macrolide (ermB and ermF), aminoglycoside (strA and aac(6')-Ib-cr), and integron-associated (intI1). The resistance classes most relevant for ARB risk assessment included sulfonamides (sulfamethoxazole and sulfamethazine), cephalosporin (cephalothin and cefoxitin), penicillin (ampicillin), and ciprofloxin (ciprofloxacin). Considerations for exposure assessment are discussed to highlight risk assessment needs relating to antimicrobial resistance (AMR) associated with biosolids application. This study aids in prioritization of resources for reducing the spread of AMR within a One Health framework.

Culture-based and molecular investigation of antibiotic and metal resistance in a semi-arid agricultural soil repeatedly amended with urban sewage sludge

Unsustainable agricultural intensification and climate change effects have caused chronic soil depletion in most arid and semi-arid croplands. As such, the land application of urban sewage sludge (USS) has been regulated in several countries as an alternative soil conditioner with recycling benefits. However, the risks of multi-contamination have made its agricultural reuse debatable. Accordingly, this study explored the long-term the impact of repetitive USS applications with increasing rates (0, 40, 80, and 120 t ha-1 year-1) on a sandy soil properties. A special focus was on the spread of antibiotic-resistant bacteria, metal-resistant bacteria and corresponding resistance genes in soil (ARB, MRB, ARGs and MRGs, respectively). The outcomes showed a dose-dependent variation of different soil parameters including the increase of heavy metal content and total heterotrophic bacteria (THB) up to the highest sludge application rate. Besides, the two last sludge lots applied in fall 2019 and 2020 contained cultivable ARB for all addressed antibiotics at much higher counts than in corresponding treated soils. Interestingly, the average index of antibiotic resistance (ARB/THB) increased in the USS used in fall 2020 compared to 2019 (from 6.2% to 9.4%). This indicates that factors such as fluctuations in wastewater quality, treatments operations, and extensive antibiotic use following the outbreak of the COVID-19 pandemic in early 2020 could have caused this variation. The molecular assessment of bacterial resistance resulted in the identification of three ARGs (mefA, sul1 and sul2), one MRG (czcA) and one integron (intI1). This might have implications on resistance co-selection, which can pose a threat to human health via contaminated crops.

Mitigating the health risk of antibiotic resistance genes through reductive soil disinfestation in protected agroecosystems

Soil used to grow vegetable crops is usually subjected to various soil management strategies. However, the effects of these management strategies on antibiotic resistance genes (ARGs), which have important implications for human health, are still poorly understood. Here, we examined the effects of reductive soil disinfestation (RSD) on soil ARG profiles, the composition of the bacterial community, and the interactions between ARG hosts and nonhosts in soils under different fertilization regimes. The results indicated that RSD treatment significantly decreased the relative abundance of soil ARGs and mobile genetic elements (MGEs) by 43.4 % to 61.3 %. During the following planting period, the RSD-treated soils were more susceptible to colonization by exogenous microorganisms from the composted chicken manure. Moreover, RSD treatment inhibited the transfer rate of ARGs from the soil to the plant root system and resulted in a lower proportion of ARG hosts with pathogenic ability. Notably, RSD treatment promoted cooperation among nonhost communities. The findings of our study indicated that RSD treatment significantly reduced the health risk of soil resistome. In summary, the application of RSD treatment effectively diminishes ARG pollution, thereby playing a crucial role in enhancing soil ecological health and advancing sustainable agricultural development.

Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils

Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.

The significance of environmentally bioavailable antimicrobials in driving antimicrobial resistance in soils

Antimicrobial resistance (AMR) stands as an escalating public health crisis fueled by antimicrobial residues in the environment, particularly in soil, which acts as a reservoir for antimicrobial resistance genes (ARGs). Merely quantifying the total extractable concentration of antimicrobials, instead of bioavailable fractions, may substantially underestimate their minimal selection concentration for propagating ARGs. To shed light on the role of bioavailability in ARG abundance within soil, a systematic bioavailability assessment method was established for accurately quantifying the partitioning of multi-class antimicrobials in representative Chinese soils. Microcosm studies unveiled that antimicrobials persisting in the bioavailable fraction could potentially prolong their selection pressure duration to trigger AMR. Notably, the co-occurrence of pesticide or steroid hormone influenced the development trends of ARG subtypes, with fluoroquinolone resistance genes (RGs) being particularly susceptible. Partial least squares path model (PLS-PM) analysis uncovered potentially distinct induction mechanisms of antimicrobials: observable results suggested that extractable residual concentration may exert a direct selection pressure on the development of ARGs, while bioavailable concentration could potentially play a stepwise role in affecting the abundance of mobile genetic elements and initiating ARG dissemination. Such unprecedented scrutinization of the interplay between bioavailable antimicrobials in soils and ARG abundance provides valuable insights into strategizing regulatory policy or guidelines for soil remediation.

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.

Sewage Sludge Promotes the Accumulation of Antibiotic Resistance Genes in Tomato Xylem

Xylem serves as a conduit linking soil to the aboveground plant parts and facilitating the upward movement of microbes into leaves and fruits. Despite this potential, the composition of the xylem microbiome and its associated risks, including antibiotic resistance, are understudied. Here, we cultivated tomatoes and analyzed their xylem sap to assess the microbiome and antibiotic resistance profiles following treatment with sewage sludge. Our findings show that xylem microbes primarily originate from soil, albeit with reduced diversity in comparison to those of their soil microbiomes. Using single-cell Raman spectroscopy coupled with D2O labeling, we detected significantly higher metabolic activity in xylem microbes than in rhizosphere soil, with 87% of xylem microbes active compared to just 36% in the soil. Additionally, xylem was pinpointed as a reservoir for antibiotic resistance genes (ARGs), with their abundance being 2.4-6.9 times higher than in rhizosphere soil. Sludge addition dramatically increased the abundance of ARGs in xylem and also increased their mobility and host pathogenicity. Xylem represents a distinct ecological niche for microbes and is a significant reservoir for ARGs. These results could be used to manage the resistome in crops and improve food safety.

Do contaminants compromise the use of recycled nutrients in organic agriculture? A review and synthesis of current knowledge on contaminant concentrations, fate in the environment and risk assessment

Use of nutrients recycled from societal waste streams in agriculture is part of the circular economy, and in line with organic farming principles. Nevertheless, diverse contaminants in waste streams create doubts among organic farmers about potential risks for soil health. Here, we gather the current knowledge on contaminant levels in waste streams and recycled nutrient sources, and discuss associated risks. For potentially toxic elements (PTEs), the input of zinc (Zn) and copper (Cu) from mineral feed supplements remains of concern, while concentrations of PTEs in many waste streams have decreased substantially in Europe. The same applies to organic contaminants, although new chemical groups such as flame retardants are of emerging concern and globally contamination levels differ strongly. Compared to inorganic fertilizers, application of organic fertilizers derived from human or animal feces is associated with an increased risk for environmental dissemination of antibiotic resistance. The risk depends on the quality of the organic fertilizers, which varies between geographical regions, but farmland application of sewage sludge appears to be a safe practice as shown by some studies (e.g. from Sweden). Microplastic concentrations in agricultural soils show a wide spread and our understanding of its toxicity is limited, hampering a sound risk assessment. Methods for assessing public health risks for organic contaminants must include emerging contaminants and potential interactions of multiple compounds. Evidence from long-term field experiments suggests that soils may be more resilient and capable to degrade or stabilize pollutants than often assumed. In view of the need to source nutrients for expanding areas under organic farming, we discuss inputs originating from conventional farms vs. non-agricultural (i.e. societal) inputs. Closing nutrient cycles between agriculture and society is feasible in many cases, without being compromised by contaminants, and should be enhanced, aided by improved source control, waste treatment and sound risk assessments.

Determining the spatiotemporal variation, sources, and ecological processes of antibiotic resistance genes in a typical lake of the middle reaches of the Yangtze River

Antibiotic resistance genes (ARGs) are emerging environmental pollutants, influenced by complex regulatory factors. River-lake systems act as natural reservoirs for ARGs and provide an ideal model for studying their regulatory mechanisms. This study employed high-throughput quantitative PCR, high-throughput sequencing, correlation analyses, and model predictions to investigate the dynamics of ARGs and their influencing factors in Liangzi Lake, located in the mid-reaches of the Yangtze River. The research specifically centered on three environmental components: lake water, sediment, and river water. Results indicated that the ARGs from eight major antibiotic classes, displaying distinct seasonal distribution patterns. In comparison to the sediment, the water phase demonstrated a higher diversity of ARGs, with the highest level of ARGs sharing observed between lake and river waters (approximately 83.7 %). Furthermore, seasonal variations significantly influenced the distributions of both ARGs and bacterial communities. The diversity of ARGs was highest during the summer and autumn, and specific bacterial species exhibited robust correlations with ARGs (including matA/mel, aac (6')-Ib-03, and blaROB). It is worth noting that environmental attributes and bacterial diversity had the most substantial impact on the dynamic changes in ARGs. Lastly, source tracking analysis pinpointed that sediment as the primary source of ARGs in lake water, constituting 45 % to 48 % of the total ARGs. Our study provides a comprehensive analysis of ARGs and their influencing factors in the river-lake system of the middle reaches of the Yangtze River, with Liangzi Lake as a representative case.

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

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

Prevalence of antibiotic and metal resistance genes in phytoremediated cadmium and zinc contaminated soil assisted by chitosan and Trichoderma harzianum

Heavy metal in soil have been shown to be toxic with high concentrations and acts as selective pressure on both bacterial metal and antibiotic resistance determinants, posing a serious risk to public health. In cadmium (Cd) and zinc (Zn) contaminated soil, chitosan (Chi) and Trichoderma harzianum (Tri) were applied alone and in combination to assist phytoremediation by Amaranthus hypochondriacus L. Prevalence of antibiotic and metal resistance genes (ARGs and MRGs) in the soil was also evaluated using metagenomic approach. Results indicated that the phytoremediation of Cd and Zn contaminated soil was promoted by Chi, and Tri further reinforced this effect, along with the increased availability of Cd and Zn in soil. Meanwhile, combination of Chi and Tri enhanced the prevalence of ARGs (e.g., multidrug and β-lactam resistance genes) and maintained a high level of MRGs (e.g., chromium, copper) in soil. Soil available Zn and Cd fractions were the main factors contributing to ARGs profile by co-selection, while boosted bacterial hosts (e.g., Mitsuaria, Solirubrobacter, Ramlibacter) contributed to prevalence of most MRGs (e.g., Cd). These findings indicate the potential risk of ARGs and MRGs propagation in phytoremediation of metal contaminated soils assisted by organic and biological agents.

Comprehensive profiling and risk assessment of antibiotic resistance genes in a drinking water watershed by integrated analysis of air-water-soil

The prevalence of antibiotic resistance genes (ARGs) in diverse habitats threatens public health. Watersheds represent critical freshwater ecosystems that interact with both the soil and atmosphere. However, a holistic understanding of ARGs distribution across these environmental media is currently inadequate. We profiled ARGs and bacterial communities in air-water-soil in the same watershed area during four seasons using high-throughput qPCR and 16S rRNA gene sequencing. Our findings demonstrated that aminoglycoside resistance genes (58.5%) were dominant in water, and multidrug resistance genes (55.2% and 54.2%) were dominant in soil and air. Five ARGs and nineteen bacterial genera were consistently detected in all samples, were named as shared genes or bacteria. Co-occurrence Network analysis revealed the co-occurrence module of resistance genes, mobile genetic elements (MGEs), and potential bacterial hosts, indicating that shared genes and bacteria may persist and co-spread across different environmental media. The risk assessment framework, based on ARGs' abundance, detection rate, and mobility, identified 33 high-risk ARGs. This is essential to evaluate the health risks of ARGs and to develop strategies to limit the threat of antibiotic resistance. Our study offers new insights into the risks associated with ARGs in the environment and suggests that ARGs may depend on specific bacterial cohabitants that co-exist with MGEs to facilitate their spread across environmental interfaces.

Nitrogen-doped graphene for tetracycline removal via enhancing adsorption and non-radical persulfate activation

Nitrogen-doped graphene (NG) was synthesized via direct thermal annealing treatment. The obtained NG showed outstanding removal ability for tetracycline (TC) ascribed to enhanced adsorption and persulfate activation. The maximum TC adsorption capacity calculated from the Langmuir model of NG was 227.3 mg/g, which was 1.66 times larger than nitrogen-free graphene. The coexistence of NG and persulfate (PS) exhibited complete degradation of TC within 120 min attributed to the successful modification of nitrogen. Further analysis demonstrated that non-radical electron transfer was the dominant degradation pathway, which was different from the widely acknowledgeable radical mechanism. An electron donor-mediator-acceptor system was introduced, in which TC, NG, and PS performed as electron donor, mediator, and acceptor, respectively. The potential intermediates in the TC degradation process were detected and toxicity assessment was also performed. In addition, more than 75.8% of total organic carbon was removed, and excellent reusability was manifested in multiple adsorption and degradation experiments.

Long-term field application of manure induces deep selection of antibiotic resistomes in leaf endophytes of Chinese cabbage

Antibiotic resistomes in leaf endophytes of vegetables threaten human health through the food chain. However, little is known about the ability of long-term manure fertilization to impact the deep selection of antibiotic resistance genes (ARGs) in leaf endophytes of vegetables planted in different types of soils. Here, by high-throughput quantitative PCR, we characterized the ARGs of leaf endophytes of Chinese cabbage (Brassica pekinensis (Lour.) Rupr.) grown in long-term (14 year) manure-amended acidic, neutral and calcareous soils. In total, 87 ARGs and 4 mobile genetic elements (MGEs) were detected in all the samples. Manure fertilization significantly increased the ARG numbers and normalized abundance in leaf endophytes, especially in acidic soil. Moreover, in acidic soil, manure application also led to a higher increase in the normalized abundance of opportunist and specialist ARGs, and more opportunist and specialist ARGs posed a high risk according to their risk ranks. Random forest analysis revealed that Proteobacteria and MGEs were the major drivers affecting the normalized abundance of opportunist and specialist ARGs in both acidic and neutral soils, respectively. In calcareous soil, Cyanobacteria and Actinobacteria were the most important contributors. Collectively, this study expands our knowledge about the deep selection of plant resistomes under long-term manure application.

Increasing Antimicrobial Resistance and Potential Human Bacterial Pathogens in an Invasive Land Snail Driven by Urbanization

Our understanding of the role urbanization has in augmenting invasive species that carry human bacterial pathogens and antimicrobial resistance (AMR) remains poorly understood. Here, we investigated the gut bacterial communities, antibiotic resistance genes (ARGs) and potential antibiotic-resistant pathogens in giant African snails (Achatina fulica) collected across an urbanization gradient in Xiamen, China (n = 108). There was a lack of correlation between the microbial profiles of giant African snails and the soils of their habitats, and the resistome and human-associated bacteria were significantly higher than those of native snails as well as soils. We observed high diversity (601 ARG subtypes) and abundance (1.5 copies per 16S rRNA gene) of giant African snail gut resistome. Moreover, giant African snails in more urban areas had greater diversity and abundance of high-risk ARGs and potential human bacterial pathogens (e.g., ESKAPE pathogens). We highlight that urbanization significantly impacted the gut microbiomes and resistomes of these invasive snails, indicating that they harbor greater biological contaminants such as ARGs and potential human bacterial pathogens than native snails and soils. This study advances our understanding of the effect of urbanization on human bacterial pathogens and AMR in a problematic invasive snail and should help combat risks associated with invasive species under the One Health framework.

Composting reduces the risks of antibiotic resistance genes in maize seeds posed by gentamicin fermentation waste

Using high-throughput quantitative PCR and next generation sequencing, the impact of land application of raw and composted gentamicin fermentation waste (GFW) on antibiotic resistance genes (ARGs) in maize seeds was studied in a three-year field trial. The raw and composted GFW changed both the bacterial community composition and the ARGs diversity in the maize seeds compared to non-amended controls and chemical fertilizer. The abundance of ARGs after raw GFW amendment was significantly higher than other treatments because of a high abundance of aadA1, qacEdeltal and aph(2')-Id-02; probably induced by gentamicin selection pressure in maize tissues. Meanwhile, the potential host of these three ARGs, pathogenic bacteria Tenacibaculum, also increased significantly in maize seeds after the application of raw GFW. But our result proved that composting could weaken the risk posed by GFW. We further reveal that the key biotic driver for shaping the ARG profiles in maize seeds is bacterial community followed by heavy metal resistance genes, and ARGs are more likely located on bacterial chromosomes. Our findings provide new insight into ARGs dispersal mechanism in maize seeds after long-term GFW application, demonstrate the potential benefits of composting the GFW to reduce risks as well as the potential efficient management method to GFW.

Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks

As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.

Global profiling of antibiotic resistomes in maize rhizospheres

The spreading of antimicrobial resistance (AMR) in crops and food products represents a global concern. In this study, we conducted a survey of resistomes in maize rhizosphere from Michigan, California, the Netherlands, and South Africa, and investigated potential associations with host bacteria and soil management practices in the crop field. For comparison, relative abundance of antibiotic resistance genes (ARGs) is normalized to the size of individual metagenomes. Michigan maize rhizosphere metagenomes showed the highest abundance and diversity of ARGs, with the detection of blaTEM-116, blaACT-4/-6, and FosA2, exhibiting high similarity (≥ 99.0%) to those in animal and human pathogens. This was probably related to the decade-long application of manure/composted manure from antibiotic-treated animals. Moreover, RbpA, vanRO, mtrA, and dfrB were prevalently found across most studied regions, implying their intrinsic origins. Further analysis revealed that RbpA, vanRO, and mtrA are mainly harbored by native Actinobacteria with low mobility since mobile genetic elements were rarely found in their flanking regions. Notably, a group of dfrB genes are adjacent to the recombination binding sites (attC), which together constitute mobile gene cassettes, promoting the transmission from soil bacteria to human pathogens. These results suggest that maize rhizosphere resistomes can be distinctive and affected by many factors, particularly those relevant to agricultural practices.

Microplastic contamination of soil: Are input pathways by compost overridden by littering?

Compost application is a widely recommended agricultural practice to improve soil fertility. As almost all compost is likely polluted with plastic we hypothesize that compost application is a major input pathway for microplastics (MPs) into agricultural soil. To attribute the plastic load of soil to compost application, we investigated MPs in topsoil (0-30 cm) of a controlled, long-term fertilizer trial with application of compost made of municipal biowaste (0, 5, 10, and 20 t ha^-1a^-1), which ended 11 years ago. Microplastics were analyzed via density separation (ZnCl₂) and light microscopy; testing this method recovered 92 ± 10 % of spiked plastic items. The fields of the long-term compost trial showed a MP load of 0-64 items kg^-1, corresponding to MP stocks in the plough layer (0-30 cm) that ranged from 38.2 ± 55.5 million to 171.4 ± 57.5 million items ha^-1. Microplastic stocks and contents increased with increasing amount of compost application. Thus, we confirm compost as a major input pathway for MPs into agricultural soil, with the effect still visible after 11 years. Comparison of calculated plastic input based on MP contents of recent German compost with MP loads found in soil revealed that overall compost application explained <6 % of total MP stocks. We assume that compost applied in earlier days contained higher plastic loads than recent ones, reflecting current awareness and successful efforts in reducing plastic loads during compost production. However, as the plots at the border of the field had up to 18 times higher MP loads than the inner plots of the trial, we suggest that littering also contributed significantly to MP pollution. Thus, even if given compost applications still add plastics to environment, other sources such as littering can already have become the dominating input pathway.

Exploring antibiotic resistance load in paddy-upland rotation fields amended with commercial organic and chemical/slow release fertilizer

Agricultural fertilization caused the dissemination of antibiotic resistance genes (ARGs) in agro-ecological environment, which poses a global threat to crop-food safety and human health. However, few studies are known about the influence of different agricultural fertilization modes on antibiotic resistome in the paddy-upland rotation soils. Therefore, we conducted a field experiment to compare the effect of different fertilization (chemical fertilizer, slow release fertilizer and commercial organic fertilizer replacement at various rates) on soil antibiotic resistome in paddy-upland rotation fields. Results revealed that a total of 100 ARG subtypes and 9 mobile genetic elements (MGEs) occurred in paddy-upland rotation soil, among which MDR-ARGs, MLSB-ARGs and tet-ARGs were the dominant resistance determinants. Long-term agricultural fertilization remarkably facilitated the vertical accumulation of ARGs, in particular that bla _ampC and tetO in relative abundance showed significant enrichment with increasing depth. It's worth noting that slow release fertilizer significantly increased soil ARGs, when comparable to manure with 20% replacing amount, but chemical fertilizer had only slight impact on soil ARGs. Fertilization modes affected soil microbial communities, mainly concentrated in the surface layer, while the proportion of Proteobacteria with the highest abundance decreased gradually with increasing depth. Furthermore, microbial community and MGEs were further proved to be essential factors in regulating the variability of ARGs of different fertilization modes by structural equation model, and had strong direct influence (λ = 0.61, p < 0.05; λ = 0. 55, p < 0.01). The results provided scientific guidance for reducing the spreading risk of ARGs and control ARG dissemination in agricultural fertilization.

Short-term inhalation exposure evaluations of airborne antibiotic resistance genes in environments

Antibiotic resistance is a sword of Damocles that hangs over humans. In regards to airborne antibiotic resistance genes (AARGs), critical knowledge gaps still exist in the identification of hotspots and quantification of exposure levels in different environments. Here, we have studied the profiles of AARGs, mobile genetic elements (MGEs) and bacterial communities in various atmospheric environments by high throughput qPCR and 16S rRNA gene sequencing. We propose a new AARGs exposure dose calculation that uses short-term inhalation (STI). Swine farms and hospitals were high-risk areas where AARGs standardised abundance was more abundant than suburbs and urban areas. Additionally, resistance gene abundance in swine farm worker sputum was higher than that in healthy individuals in other environments. The correlation between AARGs with MGEs and bacteria was strong in suburbs but weak in livestock farms and hospitals. STI exposure analysis revealed that occupational intake of AARGs (via PM₁₀) in swine farms and hospitals were 110 and 29 times higher than in suburbs, were 1.5 × 10⁴, 5.6 × 10⁴ and 5.1 × 10² copies, i.e., 61.9%, 75.1% and 10.7% of the overall daily inhalation intake, respectively. Our study comprehensively compares environmental differences in AARGs to identify high-risk areas, and forwardly proposes the STI exposure dose of AARGs to guide risk assessment.

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

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

Soil antibiotic abatement associates with the manipulation of soil microbiome via long-term fertilizer application

The effects of different fertilization on microbial communities and resistome in agricultural soils with a history of fresh manure application remains largely unclear. Here, soil antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and microbial communities were deciphered using metagenomics approach from a long-term field experiment with different fertilizer inputs. A total of 541 ARG subtypes were identified, with Multidrug, Macrolides-Lincosamides-Streptogramins (MLS), and Bacitracin resistance genes as the most universal ARG types. The abundance of ARGs detected in manure (2.52 ARGs/16 S rRNA) treated soils was higher than chemical fertilizer (2.42 ARGs/16 S rRNA) or compost (2.37 ARGs/16 S rRNA) amended soils. The higher abundance of MGEs and the enrichment of Proteobacteria were observed in manure treated soils than in chemical fertilizer or compost amended soils. Proteobacter and Actinobacter were recognized as the main potential hosts of ARGs revealed by network analysis. Further soil pH was identified as the key driver in determining the composition of both microbial community and resistome. The present study investigated the mechanisms driving the microbial community, MGEs and ARG profiles of long-term fertilized soils with ARGs contamination, and our findings could support strategies to manage the dissemination of soil ARGs.

Intra-/extra-cellular antibiotic resistance responses to sewage sludge composting and salinization of long-term compost applied soils

Municipal sewage sludge, a reservoir of antibiotic resistance genes (ARGs), is usually composted as fertilizer for agricultural application especially in arid and semi-arid areas. The evolution patterns of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) during composting and their responses to soil salinization after long-term compost application kept unclear previously, which were systematically studied in the current study. The variation and dissemination risk of eARGs and iARGs with the salinization of farmland soils was also evaluated. Extra/intra-cellular ARGs relative abundance varied drastically through composting process. Generally, the relative abundance of the cell-free eARGs (f-eARGs) and the cell-adsorbed eARGs (a-eARGs) were 4.62 and 3.54 folds (median) higher than that of iARGs, respectively, during the entire composting process, which held true even before the sludge composting (false discovery rate, FDR p < 0.05). There was no significant difference in relative abundance between f-eARGs and a-eARGs. The relative abundance of eARGs gradually decreased with composting time but was relatively higher than iARGs. It was worth noting that iARGs rebounded in the maturation phase. However, an over ten-year application of the eARG-rich compost led to much more severe contamination of iARGs than eARGs in soil. Soil salinization caused remarkable rise of eARGs by 943.34-fold (FDR p < 0.05). The variation of ARGs during composting and soil salinization was closely related to the change of microbial community structure. In compost, the bacterial communities mainly interacting with ARGs were the Firmicutes (54 unique and 35 shared core genera); and the bacterial communities playing major roles in ARGs during soil salinization were Proteobacteria (116 unique and 53 shared core genera) and Actinobacteria (52 unique and 27 shared core genera). These findings are important for assessing the transmission risk of ARGs in compost application to farmland in arid and semi-arid areas.

Leaching risks of antibiotic resistance genes in urban underlying surface sediments during the simulated stormwater runoff and its controls

Recently, increasing attention has been paid to antibiotic resistance genes (ARGs) in urban stormwater runoff. However, no available literature could be found on ARGs leaching from urban underlying surface sediments during stormwater runoff. In this study, surface sediments from commercial public squares around Nanjing (China) was selected for the investigation of target ARGs leaching kinetics, showing that absolute abundances of target ARGs desorption reached at the equilibrium during leaching time of 120-240min with all of the desorption efficiencies about 30%, indicating that there would be low proportion of leaching ARGs in the total ARGs migrating with runoff during rainfall events. Five target ARGs leaching including intI1 (clinic), strA, strB, tetM and tetX can be better described by the pseudo-second-order equation, while qacEdelta1 leaching can be better described by the pseudo-first-order equation, and the leaching for both sul1 and sul2 can be well described by the pseudo-first-order and pseudo-second-order equations. The effects of environmental factors including S/L ratios, pH values and water temperatures indicated that leaching efficiencies of target ARGs enhanced significantly with the increase of S/L ratios and water temperatures, but decreased with the increase of pH values. The transmission experiments after the simulated solar irradiation and heat implied that both large solar UV irradiation (30W/m²) and high temperature (40℃) were conducive to conjugation and transformation frequencies of ARGs. Furthermore, both high Cao and medium PAM levels could be effective for blocking ARGs transmission in the leachate from underlying surface sediments.

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.

Can radicals-orientated chemical oxidation improve the reduction of antibiotic resistance genes (ARGs) by mesophilic anaerobic digestion of sludge?

The dissemination of antibiotic resistance genes (ARGs) increases risks towards human health and environmental safety. This work investigates the control of ARGs abundance and bacterial community evolution involved in waste activated sludge (WAS) treatment by chemical conditioning and subsequent mesophilic anaerobic digestion (MAD). The different chemical oxidation processes of ferrous iron-activated oxone and hydrogen peroxide (PMS-Fe²⁺ and H₂O₂-Fe²⁺) and thermal-activated oxone (PMS@80 ℃) were investigated, and the ferric chloride (FeCl₃) and inactivated oxone (PMS) were compared. PMS@80 ℃ decreased the absolute abundance of most ARGs by 10.6-99.3% and that of total ARGs by 66.3%. Interestingly, oxidation pretreatment increased rather than decreased the relative abundance of most ARGs. MAD with PMS@80 ℃ pretreatment increased the absolute abundance of total ARGs by 51.6%, and other MAD processes decreased it by 8.6-47.4%. PMS-Fe²⁺ and PMS@80 ℃ negatively inhibited methane production from 98.3 to 81.7 and 94.4 mL/g VSS in MAD. MAD effluent showed high abundance of Arcobacter genus in the range of 8.1-17.4% upon PMS-based pretreatment, possibly related to sulfur oxidation, nitrate reduction, and blaVEB enrichment. The radicals-orientated chemical oxidation can hardly improve the ARGs elimination by MAD due to the extremely high competitive organics in sludge.

Fate of bacterial community, antibiotic resistance genes and gentamicin residues in soil after three-year amendment using gentamicin fermentation waste

Over a three-year field trial, the impacts of composted and raw gentamicin fermentation waste (GFW) application to land on residual soil gentamicin levels, physicochemical properties, bacterial community composition, and antibiotic resistance genes (ARGs) were assessed. In the saline-alkali soil tested, GFW application decreased electrical conductivity (EC) and pH. Importantly, there was no measurable long-term accumulation of gentamicin as a result of GFW addition. Changes in the abundance of Bacillus was primarily associated with degradation of gentamicin in soil, whereas wider (i.e. more general) shifts in bacterial communities over the treatments was linked to alteration of soil physicochemical properties, particularly pH, total nitrogen, dissolved organic carbon, EC, NO₃^--N and NH₄⁺-N. Compared with other treatments, soils receiving composted GFW harbored more types of ARGs and significantly higher (P < 0.05) abundances of mobile genes elements (MGEs) (especially IncQ and Int1) and aminoglycoside ARGs (especially aminoglycoside phosphotransferases genes, APH). Finally, the abundances of ARGs in soils receiving raw and composted GFW were 59.60% and 50.26% higher than that in soils only receiving chemical fertilizer, respectively. Specifically, the abundances of APH, especially strB, were significantly higher than other kinds of ARGs (P < 0.05). The results of linear regression and partial least squares path model showed that MGEs, including plasmids, integrons, and transposons, along with soil properties (EC and NH₄⁺-N) were the main factors associated with change in ARGs. Furthermore, different MGEs were involved in different transfer mechanisms of specific ARGs. Our findings demonstrated the potential risks of using raw and composted GFW as fertilizer, and suggest potential solutions to this problem.

Implications for mitigation of antibiotic resistance: Differential response of intracellular and extracellular antibiotic resistance genes to sludge fermentation coupled with thermal hydrolysis

Thermal hydrolysis pretreatment (THP) can effectively remove the antibiotic resistance genes (ARGs) from sewage sludge, but the rebounding effects in the subsequent anaerobic fermentation are often observed. The purpose of this study was to elucidate the distribution and fate of intracellular and extracellular ARGs (iARGs and eARGs) in the sludge acidogenic fermentation process coupled with THP. Our results revealed that THP significantly reduced the absolute abundance of total ARGs in raw sludge but increased eARGs by 0.3-1.4 log units under practical conditions (140 °C for 30 min). There is no significant difference in the removal of total ARGs between the two acidogenic fermenters receiving raw and hydrolyzed sludge, with iARGs prevailing in the produced biosolids. The succession of bacterial community and the co-occurrence relationships among ARG type, mobile genetic elements and bacterial taxa were observed, suggesting a phylogenetic basis for the iARGs patterns in fermented sludge. However, eARGs were susceptible to biodegradation with a half-life of 2.34 h and they contributed limitedly to the ARGs propagation through transformation. These findings suggest an emphasis on the mitigation of iARGs during the acidogenic fermentation of sludge, which would be achieved by lowering the richness and physicochemical destruction of potential hosts.

Enhanced transformation of sulfamethoxazole by birnessite in the presence of gallic acid: Kinetics and pathways

The emergence of antibiotic agents like sulfamethoxazole (SMX) in soils and surface water can cause serious threat to human and animal health. In this work, mechanisms for the promotive effect of gallic acid (GA) on the transformation of SMX by birnessite were studied. In the absence of GA, the observed pseudo-first-order reaction constants (k_obs) decreased as the pH increased from 4.0 to 8.0, in agreement with the decrease in redox potential of birnessite with increasing pH. The changes in chemical state of surface Mn atoms suggested that Mn(IV) played a major role in SMX transformation. SMX was transformed mainly by the bond cleavage of SN and SC, NH oxidation, and self- or cross-coupling reactions, with the formation of seven transformation products. The presence of GA could significantly promote the transformation of SMX, which was more pronounced at pH 6.0 comparing to the effect observed at 4.0. This promotive effect was attributed to both the addition reactions between SMX and GA quinones and the condensation reactions between -COOH of quinones and -NH₂ of SMX or its transformation products. Moreover, the addition reaction between SMX and OH coming from the GA oxidation by birnessite was also proposed, while its contribution to SMX transformation was small. Furthermore, pyrogallol and methyl gallate that do not contain electron-withdrawing substituent like -COOH group are less effective in promoting SMX transformation than GA, suggesting the electron-density of β‑carbon is key to the occurrence of addition reaction. Our results demonstrate the important role of birnessite and naturally occurring phenolic acids in abiotic transformation SMX, which will profoundly affect its mobility and bioavailability in environments.

Advancements in detection and removal of antibiotic resistance genes in sludge digestion: A state-of-art review

Sludge from wastewater treatment plants can act as a repository and crucial environmental provider of antibiotic resistance genes (ARGs). Over the past few years, people's knowledge regarding the occurrence and removal of ARGs in sludge has broadened remarkably with advancements in molecular biological techniques. Anaerobic and aerobic digestion were found to effectively achieve sludge reduction and ARGs removal. This review summarized advanced detection and removal techniques of ARGs, in the last decade, in the sludge digestion field. The fate of ARGs due to different sludge digestion strategies (i.e., anaerobic and aerobic digestion under mesophilic or thermophilic conditions, and in combination with relevant pretreatment technologies (e.g., thermal hydrolysis pretreatment, microwave pretreatment and alkaline pretreatment) and additives (e.g., ferric chloride and zero-valent iron) were systematically summarized and compared in this review. To date, this is the first review that provides a comprehensive assessment of the state-of-the-art technologies and future recommendations.

Bioleaching rather than chemical conditioning using Fe[III]/CaO or polyacrylamide mitigates antibiotic resistance in sludge composting via pre-removing antibiotic resistance genes and limiting horizontal gene transfer

Conditioning can drastically improve the dewaterability of sewage sludge and is widely practiced in most wastewater treatment plants (WWTPs). Sludge conditioning was also reported as a crucial step in sludge treatment to attenuate antibiotic resistance, but it remains unclear whether the attenuated antibiotic resistance by conditioning treatments would guarantee low abundance of antibiotic resistance genes (ARGs) in the compost products of municipal sewage sludge. Herein, the impacts of three conditioning treatments, including bioleaching and chemical conditioning using Fe[III]/CaO or polyacrylamide (PAM), on the abundances of 20 ARGs and 4 mobile genetic elements (MGEs) during conventional aerobic composting of dewatered sludge were investigated. It was found that the absolute and relative abundances of total ARGs in compost product of bioleached sludge accounted for only 13.8%-28.8% of that in compost products of un-conditioned, Fe[III]/CaO-conditioned, or PAM-conditioned sludges. Besides, bioleaching conditioning resulted in the lowest abundances of ARG subtypes and ARG-associated bacteria in the sludge compost product. The shift of ARG profiles in the bioleached sludge composting can be mainly ascribed to the ARG-associated bacteria, while the MGEs drove the ARG profiles during conventional composting of un-conditioned sludge and the two chemically conditioned sludge. Thus, bioleaching conditioning is superior to the chemical conditioning using Fe[III]/CaO or PAM in mitigating antibiotic resistance in sludge compost products, which was contributed by the pre-removal of ARGs prior to composting treatment and the potential limitation of ARGs transfer during conventional composting.

Strategy for Mitigating Antibiotic Resistance by Biochar and Hyperaccumulators in Cadmium and Oxytetracycline Co-contaminated Soil

The global prevalence of antibiotic resistance genes (ARGs) is of increasing concern as a serious threat to ecological security and human health. Irrigation with sewage and farmland application of manure or biosolids in agricultural practices introduce substantial selective agents such as antibiotics and toxic metals, aggravating the transfer of ARGs from the soil environment to humans via the food chain. To address this issue, a hyperaccumulator (Sedum plumbizincicola) combined with biochar amendment was first used to investigate the mitigation of the prevalence of ARGs in cadmium and oxytetracycline co-contaminated soil by conducting a pot experiment. The addition of biochar affected the distribution of ARGs in soil and plants differently by enhancing their prevalence in the soil but restraining transmission from the soil to S. plumbizincicola. The planting of S. plumbizincicola resulted in an increase in ARGs in the soil environment. A structural equation model illustrated that mobile genetic elements played a dominant role in shaping the profile of ARGs. Taken together, these findings provide a practical understanding for mitigating the prevalence of ARGs in this soil system with complex contamination and can have profound significance for agricultural management in regard to ARG dissemination control.

Strategies to Control Human Health Risks Arising from Antibiotics in the Environment: Molecular Modification of QNs for Enhanced Plant-Microbial Synergistic Degradation

In the present work, a comprehensive screening and evaluation system was established to improve the plant-microbial synergistic degradation effects of QNs. The study included the construction of a 3D-QSAR model, the molecular modification, environmental friendliness and functional evaluation of drugs, degradation pathway simulation, and human health risk assessment. Molecular dynamics was applied to quantify the binding capacity of QNs toward the plant degradation enzyme (peroxidase) and microbial degradation enzymes (manganese peroxidase, lignin peroxidase, and laccase). The fuzzy comprehensive evaluation method was used in combination with the weighted average method for normalization and assigning equal weights to the plant and microbial degradation effect values of the QNs. Considering the synergistic degradation effect value as the dependent variable and the molecular information of the QNs as the independent variable, a 3D-QSAR model was constructed for the plant-microbial synergistic degradation effect of QNs. The constructed model was then employed to conduct the molecular modification, environmental friendliness and functional evaluation, degradation pathway simulation, and human health risk assessment of transformation products using pharmacokinetics and toxicokinetics. The results revealed that the synergistic degradation effect 3D-QSAR (CoMSIA) model exhibited good internal and external prediction ability, fitting ability, stability, and no overfitting phenomenon. Norfloxacin (NOR) was used as the target molecule in the molecular modification. A total of 35 NOR derivatives with enhanced plant-microbial synergistic degradation effect (1.32-21.51%) were designed by introducing small-volume, strongly electronegative, and hydrophobic hydrogen bond receptor groups into the active group of the norfloxacin structure. The environment-friendliness and the functionality of NOR were evaluated prior to and after the modification, which revealed seven environment-friendly FQs derivatives exhibiting moderate improvement in stability and bactericidal efficacy. The simulation of the NOR plant and microbial degradation pathways prior to and after the modification and the calculation of the reaction energy barrier revealed Pathway A (D-17 to D-17-2) and Pathway B (D-17 to D-17-4) as the most prone degradation pathways in plants and Pathway A (D-17 to D-17-1) and Pathway B (D-17 to D-17-4) as the most prone degradation pathways in microorganisms. This demonstrated that the degradation of the modified NOR derivatives was significantly enhanced, with the hydroxylation and piperazine ring substitution reaction playing an important role in the degradation process. Finally, the parameters, including hepatotoxicity, mutagenicity, and rodent carcinogenicity, among others, predicted using the pharmacokinetics and toxicokinetics analyses revealed a significant reduction in the human health risk associated with the modified NOR, along with a considerable reduction in the toxicity of its transformation products, implying that the human health risk associated with the transformation products was reduced remarkably. The present study provides a theoretical basis for novel ideas and evaluation programs for improving the plant-microbial synergistic degradation of the QNs antibiotics for source control and drug design, thereby reducing the residues of these antibiotics and the associated hazard in the complex plant-soil environment, ultimately decreasing the potential risks to human health.

Insights into the mechanism of the interference of sulfadiazine on soil microbial community and function

The accumulation of sulfonamides in the soil environment possessed the potential to change soil microbial community and function. Metabolomics is capable of providing insights into the carbon metabolic pool and molecular mechanisms associated with external stressors. Here we evaluated alternations in soil bacterial community and soil metabolites profiles under sulfadiazine (SDZ) exposure and proposed a potential mechanism that SDZ accumulation in soil affected soil organic matter (SOM) cycling. Sequencing analysis showed that the relative abundance of bacterial species associated with carbon cycling significantly decreased under high concentrations of SDZ exposure. Untargeted metabolomics analysis showed that 78 metabolites were significantly changed with the presence of SDZ in soil. The combination of functional predictions and pathway analysis both demonstrated that high concentrations of SDZ exposure could cause disturbance in anabolism and catabolism. Moreover, the noticeable decline in the relative content of carbohydrates under high concentrations of SDZ exposure might weaken physical separation and provide more chances for microbes to degrade SOM. The above results provided evidence that SDZ accumulation in soil held the potential to disturb SOM cycling. These findings spread our understanding about the environmental risk of antibiotic in the soil environment beyond the dissemination of antibiotic resistance.

Soil type shapes the antibiotic resistome profiles of long-term manured soil

Animal manure fertilization facilitates the proliferation and dissemination of antibiotic resistance genes (ARGs) in soil, posing high risks to humans and ecosystem health. Although studies suggest that soil types could shape the ARG profiles in greenhouse soil, there is still a lack of comparative studies on the fate of ARGs in different types of manured soils under field trials. Thus, a metagenomic approach was used to decipher the fate of ARGs in 12-year long-term fertilized (inorganic fertilizer, compost manure and a mix of them) acidic, near-neutral and alkaline soils. A total of 408 unique ARG subtypes with multidrug, glycopeptide, beta-lactam and aminoglycoside resistance genes were identified as the most universal ARG types in all soil samples. Genes conferred to beta-lactam was the predominant ARG type in all the manure-amended soils. Genomic and statistical analyses showed that manure application caused the enrichment of 98 and 91 ARG subtypes in acidic and near-neutral soils, respectively, and 8 ARG subtypes in alkaline soil. The abundances of Proteobacteria (acidic and near-neutral soils) and Actinobacteria (alkaline soil), which are the potential hosts of ARGs, were clearly increased in manured soils. Random forest modelling and Pearson correlation analysis revealed that the soil properties (pH and bio-available Zn) and mobile genetic elements had considerable impacts on the transmission of ARGs. A structural equation model further indicated that soil types shaped the ARG profiles by significantly (P < 0.01) influencing the soil properties, bacterial abundance and bacterial diversity, where bacterial abundance was the major factor influencing the ARG profiles. This study systematically explored the mechanisms shaping the ARG profiles of long-term manured soils, and this information could support strategies to manage the dissemination of ARGs in different soil types.

Antibiotic Resistance Gene Transformation and Ultrastructural Alterations of Lettuce (Lactuca sativa L.) Resulting from Sulfadiazine Accumulation in Culture Solution

The research herein explored the possible mechanism of toxicity of the antibiotic sulfadiazine (SD) and the related antibiotic resistance gene transformation in lettuce by systematically investigating its growth responses, ultrastructural changes, and antibiotic resistance gene transformation via solution culture experiments. The results showed that SD mainly accumulated in the roots of lettuce at concentrations ranging from 6.48 to 120.87 μg/kg, which were significantly higher than those in leaves (3.90 to 16.74 μg/kg). Lower concentrations of SD (0.5 and 2.0 mg/L) in the culture nutrient solution exerted little effect on lettuce growth, while at SD concentrations higher than 10 mg/L, the growth of lettuce was significantly inhibited, manifesting as shorter root length and lower dry matter yield of whole lettuce plants. Compared with that for the control group, the absolute abundance of bacteria in the root endophyte, rhizosphere, and phyllosphere communities under different concentrations of SD treatment decreased significantly. sul1 and sul2 mainly accumulated in the root endophyte community, at levels significantly higher than those in the leaf endophyte community. Studies of electrolyte leakage and ultrastructural characteristics of root and leaf cells indicated that lettuce grown in culture solutions with high SD concentrations suffered severe damage and disintegration of the cell walls of organs, especially chloroplasts, in leaves. Furthermore, the possible mechanism of SD toxicity in lettuce was confirmed to start with the roots, followed by a free flow of SD into the leaves to destroy the chloroplasts in the leaf cells, which ultimately reduced photosynthesis and decreased plant growth. Studies have shown that antibiotic residues have negative effects on the growth of lettuce and highlight a potential risk of the development and spread of antibiotic resistance in vegetable endophyte systems.

The variation of antibiotic resistance genes and their links with microbial communities during full-scale food waste leachate biotreatment processes

The prevalence of antibiotic resistance genes (ARGs) has been widely reported in various environments. However, little is known of them in food waste (FW) leachate with high organic content and how their distribution is influenced by biotreatment processes. Here, twelve ARGs, two integrase genes and bacterial communities were investigated during two full-scale FW biotreatment processes. High ARGs abundances (absolute: 1.03 × 10⁷-2.82 × 10⁹copies/mL; relative: 0.076-2.778copies/16S rRNA) were observed across all samples. Although biotreatment effectively reduced absolute abundance of ARGs, additional bacteria acquiring ARGs caused an increase in their relative abundance, which further increased the transmission risk of ARGs. mexF, blaCTX-M, sul1 played crucial roles and sul1 might be considered as an indicator for the prediction of total ARGs. It is worrying that the discharge (effluent and sludge) included highly abundant ARGs (5.09 × 10¹⁴-4.83 × 10¹⁵copies/d), integrons (1.11 × 10¹⁴-6.04 × 10¹⁴copies/d) and potential pathogens (such as Pseudomonas and Streptococcus), which should be given more attentions. blaCTX-M and tetQ possessed most potential hosts, Proteobacteria-L and Firmicutes-W were predominant contributors of ARGs-hosts at genus level. This study suggested FW leachate biotreatment systems could be reservoirs of ARGs and facilitated the proliferation of them. The exploration of effective removal methods and formulation of emission standard are necessary for future ARGs mitigation.

Characteristics of phytoplankton-zooplankton communities and the roles in the transmission of antibiotic resistance genes under the pressure of river contamination

Insight into the distribution of antibiotic resistance genes (ARGs) in phytoplankton-zooplankton communities (PZCs) is essential for the management and control of antibiotic resistance in aquatic ecosystems. This study characterized the profiles of PZCs and their carried ARGs in a typical urban river and ranked the factors (water physicochemical parameters, PZCs, bacterial abundance, and mobile genetic elements) influencing the dynamic of ARG profiles by the partial least squares path modeling. Results showed Cyanobacteria, Bacillariophyta and Chlorophyta were dominant phyla of phytoplankton, and Rotifera was with the highest abundance in zooplankton. River contamination markedly altered the structure of PZCs, increasing the abundance of phytoplankton and zooplankton, decreasing the diversity of phytoplankton while elevating in zooplankton. PZCs harbored large amounts of ARGs with average relative abundance of 2.35 × 10^-2/copies nearly an order magnitude higher than the living water and most ARGs exhibited significant accumulation in PZCs with the aggravated environmental pollution. The partial least squares path modeling predicted the water parameters as the most important factor mainly playing indirect effects on ARGs via PZCs and bacterial communities, followed by mobile genetic elements as the most essential direct factor for ARGs profiles. Besides, PZCs were also important drivers for the carried ARGs via direct effects on the ARGs' composition and indirect effects on host bacterial communities of ARGs and their mobile genetic elements. The present study fills the gaps in knowledge about the distribution of ARGs in PZCs and provided a new perspective to decipher the key roles of PZCs in the maintenance and dissemination of ARGs in urban river ecosystems.

Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage

Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.

Investigating antibiotics, antibiotic resistance genes in soil, groundwater and vegetables in relation to agricultural field - Applicated with lincomycin mycelial residues compost

Antibiotic mycelial residue, a kind of organic bio-waste, after composting with the subsequent land application is an effective way to achieve its resource utilization. However, its influences on soil quality and ecological safety in the practical agricultural field and related environmental media, e.g., groundwater and vegetables, remain investigated. In the present study, a field experiment with vegetable plants was conducted to study the influences of lincomycin mycelial residue compost (LMRC) on soil quality, and antibiotics and ARGs' fate. In particular, soil physicochemical properties and microbial community composition were analyzed. Moreover, antibiotics and ARGs' evolution in soil, vegetable, and groundwater were determined. The results showed that the LMRC amendment enhanced soil fertility with the increases of organic matter, total nitrogen, and available P/K. Enzyme activities except catalase and urease were promoted, and they were positively related to the LMRC application ratio. Soil microbial community composition presented temporary shifts as LMRC added, and the low application amount soil showed no significant difference with control at the end of the experiment. Similarly, lincomycin concentration in soil was far lower than the background, and it decreased below the predicted no-effect concentration in groundwater. Besides, the detected lincomycin in pakchoi grew in 0.5% and 1% LMRC amended soil was lower than acceptable daily intake (30 μg/kg). Low application rate (0.5%) of LMRC caused no significant changes of tested ARGs in soil, vegetables, and groundwater. Information obtained from this study provides reasonable application strategies for LMRC that with environmental acceptable antibiotic and ARGs.

Occurrence, influence and removal strategies of mycotoxins, antibiotics and microplastics in anaerobic digestion treating food waste and co-digestive biosolids: A critical review

Food waste anaerobic digestion (FWAD) can be assisted with the co-digestion of manures, agricultural waste, and sewage sludge. Nevertheless, contaminants like mycotoxins, antibiotics, and microplastics (MPs) could be introduced and negatively affect the AD system. Over 180 literatures involved the occurrence, influence and removal strategies of these three types of pollutants in AD were summarized in this review. Aflatoxin B1(AFB1) as the most concerned mycotoxins were poorly degraded and brought about inhibitions in short-term. Considering methanogenesis inhibition and occurrence concentration, the risk of oxytetracycline and norfloxacin were identified as priority among antibiotics. Leaching toxic additives from MPs could be responsible for the AD inhibition, while their materials and sizes could also prolong the acidification and methanation processes in FWAD. Strategies of bioaugmentation technologies and bioreactors to enhance the removal were suggested. Perspectives were provided for a better understanding of the fates of reviewed contaminants and their elimination in FWAD systems.

Agricultural Soils Amended With Thermally-Dried Anaerobically-Digested Sewage Sludge Showed Increased Risk of Antibiotic Resistance Dissemination

The application of sewage sludge (SS) to agricultural soil can help meet crop nutrient requirements and enhance soil properties, while reusing an organic by-product. However, SS can be a source of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), resulting in an increased risk of antibiotic resistance dissemination. We studied the effect of the application of thermally-dried anaerobically-digested SS on (i) soil physicochemical and microbial properties, and (ii) the relative abundance of 85 ARGs and 10 MGE-genes in soil. Soil samples were taken from a variety of SS-amended agricultural fields differing in three factors: dose of application, dosage of application, and elapsed time after the last application. The relative abundance of both ARGs and MGE-genes was higher in SS-amended soils, compared to non-amended soils, particularly in those with a more recent SS application. Some physicochemical parameters (i.e., cation exchange capacity, copper concentration, phosphorus content) were positively correlated with the relative abundance of ARGs and MGE-genes. Sewage sludge application was the key factor to explain the distribution pattern of ARGs and MGE-genes. The 30 most abundant families within the soil prokaryotic community accounted for 66% of the total variation of ARG and MGE-gene relative abundances. Soil prokaryotic α-diversity was negatively correlated with the relative abundance of ARGs and MGE-genes. We concluded that agricultural soils amended with thermally-dried anaerobically-digested sewage sludge showed increased risk of antibiotic resistance dissemination.

Response of soil bacterial communities to sulfadiazine present in manure: Protection and adaptation mechanisms of extracellular polymeric substances

Extracellular polymeric substances (EPS) play a dominant role in protective biofilms. However, studies exploring the underlying protective mechanism of EPS have mainly focused on activated sludge, whereas their positive roles in protecting soil microbes from environmental stress have not been elucidated. In this study, we revealed the response of soil bacterial communities to various dosages of sulfadiazine (SDZ) present in manure, with a special emphasis on the role of EPS. Sequencing analysis showed that the bacterial community demonstrated stronger symbiotic relationships and weaker competitive interaction patterns to cope with disturbance induced by SDZ. EPS was mainly composed of tyrosine-like and tryptophan-like substances, and moreover, carboxyl, hydroxyl and ether groups were the main functional groups. An adaptation mechanism, namely the enhanced secretion of tryptophan-like substances, could help alleviate the SDZ stress effectively in the biofilms occurring in soil that experienced long-term manure application. Furthermore, the existence of EPS weakened the accumulation of antibiotic resistance genes (ARGs) in soil. Our results for the first time systematically uncover the joint action of biofilm tolerance and ARGs in resisting SDZ stress, which enhances understanding of the protective role of EPS and the underlying mechanisms governing biofilm functions in soil environments.

Potential of coagulation to remove particle-associated and free-living antibiotic resistome from wastewater

Coagulation has been accepted as a cost-effective and environmental-friendly method to remove pollutants. In our recent work, two coagulants of polyaluminum chloride (PAC) and polyaluminum ferric chloride (PAFC) with dosage gradients, and one coagulant aid of anionic polyacrylamide (PAM) were used to investigate their potential to remove particle-associated (PA) and free-living (FL) ARGs and MGEs detected by high throughput qPCR (HT-qPCR) method. The results indicated that the maximum removal efficiencies of PA- and FL-ARGs (4.67- and 3.18-logs) were obtained at the PAFC dosage of 50.0 mg/L. Excessive PAFC dosage can hamper the removal of size-fractionated ARGs. As PAC aid, anionic PAM (1.0 mg/L) had limited effects to promote the removal of PA-ARG, while FL-ARG removal was enhanced by 0.34 log at the PAC dosage of 50.0 mg/L. The fitted curves suggested that the optimal chemical dosages of PAC, PAFC and PAC coupled with PAM in the removal of total ARGs and MGEs were 40.5, 64.7 and 50.0 mg/L, respectively. In addition, we found that much more coagulants were needed to remove FL-ARGs compared to that of PA-ARGs. The removal efficiencies of size-fractionated ARGs by flocculation can be affected by coagulant type, dosage, coagulant aid, Zeta potential and microorganism lifestyle (PA or FL).

Simultaneously attenuating antibiotic resistance genes and improving the dewaterability of sewage sludge by conditioning with Fenton's reagent: the pivotal role of sludge pre-acidification

Fenton conditioning processes have been recently employed to improve the dewaterability of sewage sludge. However, it remains unclear whether the conditioning with Fenton's reagent would simultaneously attenuate antibiotic resistance genes (ARGs) in sludge and improve sludge dewaterability. It was found in the present study that sludge pre-acidification played a pivotal role in simultaneously removing ARGs and improving sludge dewaterability by conditioning with Fenton's reagent. When the sewage sludge was pre-acidified to pH = 3.0 and was then conditioned using Fenton's reagent, the absolute abundances of the total ARGs and the total mobile genic elements (MGEs) in conditioned sludge were reduced by 1.85-2.10 and 2.84-3.12 log units, respectively. Additionally, sludge capillary suction time (CST) and specific resistance to filtration (SRF) were drastically reduced, and the moisture content (MC) in dewatered sludge cake was reduced to only 60.61-69.95%. Such effective attenuation of ARGs and MGEs in conditioned sludge led to their removal in both the dewatered sludge cakes and dewatering filtrate. However, only the improvement of sludge dewaterability was attained by sludge conditioning with Fenton's reagent but without sludge pre-acidification. During the conditioning treatment, the removal of loosely bound extracellular polymeric substance (EPS) and tightly bound EPS in conditioned sludge contributed to the improvement of sludge dewaterability, and the damage of sludge microbial cells was highly correlated with the attenuation of antibiotic resistance. Thus, sludge pre-acidification combined with conditioning using Fenton's reagent can be employed to simultaneously attenuate the antibiotic resistance in sewage sludge and improve sludge dewaterability.

Enrichment of antibiotic resistance genes (ARGs) in polyaromatic hydrocarbon-contaminated soils: a major challenge for environmental health

Polyaromatic hydrocarbons (PAHs) are widely spread ecological contaminants. Antibiotic resistance genes (ARGs) are present with mobile genetic elements (MGE) in the bacteria. There are molecular evidences that PAHs may induce the development of ARGs in contaminated soils. Also, the abundance of ARGs related to tetracycline, sulfonamides, aminoglycosides, ampicillin, and fluoroquinolones is high in PAH-contaminated environments. Genes encoding the efflux pump are located in the MGE and, along with class 1 integrons, have a significant role as a connecting link between PAH contamination and enrichment of ARGs. The horizontal gene transfer mechanisms further make this interaction more dynamic. Therefore, necessary steps to control ARGs into the environment and risk management plan of PAHs should be enforced. In this review, influence of PAH on evolution of ARGs in the contaminated soil, and its spread in the environment, has been described. The co-occurrence of antibiotic resistance and PAH degradation abilities in bacterial isolates has raised the concerns. Also, presence of ARGs in the microbiome of PAH-contaminated soil has been discussed as environmental hotspots for ARG spread. In addition to this, the possible links of molecular interactions between ARGs and PAHs, and their effect on environmental health has been explored.

The changes in antibiotic resistance genes during 86 years of the soil ripening process without anthropogenic activities

This study aimed to reveal the baseline of natural variations in antibiotic resistance genes (ARGs) in soil without anthropogenic activities over the decades. Nine soil samples with different time of soil formation were taken from the Yancheng Wetland National Nature Reserve, China. ARGs and mobile genetic elements (MGEs) were characterized using metagenomic analysis. A total of 196 and 192 subtypes of ARGs were detected in bulk soil and rhizosphere, respectively. The diversity and abundance of ARGs were stable during 69 years probably due to the alkaline pH soil environment but not due to antibiotics. Increases in ARGs after 86 years were probably attributed to more migrant birds inhabited compared with other sampling sites. Multidrug was the most abundant type, and largely shared by soil samples. It was further shown that soil samples could not be clearly distinguished, suggesting a slow process of succession of ARGs in the mudflat. The variation partitioning analysis revealed that the ARG profile was driven by the comprehensive effects exhibited by the bacterial community, MGEs, and environmental factors. Besides, pathogenic bacteria containing ARGs mediated by migrant birds in the area with 86 years of soil formation history nearing human settlements needed special attention. This study revealed the slow variations in ARGs in the soil ripening process without anthropogenic activities over decades, and it provided information for assessing the effect of human activities on the occurrence and dissemination of ARGs.